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1.  Combined Evidence Annotation of Transposable Elements in Genome Sequences 
PLoS Computational Biology  2005;1(2):e22.
Transposable elements (TEs) are mobile, repetitive sequences that make up significant fractions of metazoan genomes. Despite their near ubiquity and importance in genome and chromosome biology, most efforts to annotate TEs in genome sequences rely on the results of a single computational program, RepeatMasker. In contrast, recent advances in gene annotation indicate that high-quality gene models can be produced from combining multiple independent sources of computational evidence. To elevate the quality of TE annotations to a level comparable to that of gene models, we have developed a combined evidence-model TE annotation pipeline, analogous to systems used for gene annotation, by integrating results from multiple homology-based and de novo TE identification methods. As proof of principle, we have annotated “TE models” in Drosophila melanogaster Release 4 genomic sequences using the combined computational evidence derived from RepeatMasker, BLASTER, TBLASTX, all-by-all BLASTN, RECON, TE-HMM and the previous Release 3.1 annotation. Our system is designed for use with the Apollo genome annotation tool, allowing automatic results to be curated manually to produce reliable annotations. The euchromatic TE fraction of D. melanogaster is now estimated at 5.3% (cf. 3.86% in Release 3.1), and we found a substantially higher number of TEs (n = 6,013) than previously identified (n = 1,572). Most of the new TEs derive from small fragments of a few hundred nucleotides long and highly abundant families not previously annotated (e.g., INE-1). We also estimated that 518 TE copies (8.6%) are inserted into at least one other TE, forming a nest of elements. The pipeline allows rapid and thorough annotation of even the most complex TE models, including highly deleted and/or nested elements such as those often found in heterochromatic sequences. Our pipeline can be easily adapted to other genome sequences, such as those of the D. melanogaster heterochromatin or other species in the genus Drosophila.
Synopsis
A first step in adding value to the large-scale DNA sequences generated by genome projects is the process of annotation—marking biological features on the raw string of adenines, cytosines, guanines, and thymines. The predominant goal in genome annotation thus far has been to identify gene sequences that encode proteins; however, many functional sequences exist in non-protein-coding regions and their annotation remains incomplete. Mobile, repetitive DNA segments known as transposable elements (TEs) are one class of functional sequence in non-protein-coding regions, which can make up large fractions of genome sequences (e.g., about 45% in the human) and can play important roles in gene and chromosome structure and regulation. As a consequence, there has been increasing interest in the computational identification of TEs in genome sequences. Borrowing current ideas from the field of gene annotation, the authors have developed a pipeline to predict TEs in genome sequences that combines multiple sources of evidence from different computational methods. The authors' combined-evidence pipeline represents an important step towards raising the standards of TE annotation to the same quality as that of genes, and should help catalyze their understanding of the biological role of these fascinating sequences.
doi:10.1371/journal.pcbi.0010022
PMCID: PMC1185648  PMID: 16110336
2.  The use of semantic similarity measures for optimally integrating heterogeneous Gene Ontology data from large scale annotation pipelines 
Frontiers in Genetics  2014;5:264.
With the advancement of new high throughput sequencing technologies, there has been an increase in the number of genome sequencing projects worldwide, which has yielded complete genome sequences of human, animals and plants. Subsequently, several labs have focused on genome annotation, consisting of assigning functions to gene products, mostly using Gene Ontology (GO) terms. As a consequence, there is an increased heterogeneity in annotations across genomes due to different approaches used by different pipelines to infer these annotations and also due to the nature of the GO structure itself. This makes a curator's task difficult, even if they adhere to the established guidelines for assessing these protein annotations. Here we develop a genome-scale approach for integrating GO annotations from different pipelines using semantic similarity measures. We used this approach to identify inconsistencies and similarities in functional annotations between orthologs of human and Drosophila melanogaster, to assess the quality of GO annotations derived from InterPro2GO mappings compared to manually annotated GO annotations for the Drosophila melanogaster proteome from a FlyBase dataset and human, and to filter GO annotation data for these proteomes. Results obtained indicate that an efficient integration of GO annotations eliminates redundancy up to 27.08 and 22.32% in the Drosophila melanogaster and human GO annotation datasets, respectively. Furthermore, we identified lack of and missing annotations for some orthologs, and annotation mismatches between InterPro2GO and manual pipelines in these two proteomes, thus requiring further curation. This simplifies and facilitates tasks of curators in assessing protein annotations, reduces redundancy and eliminates inconsistencies in large annotation datasets for ease of comparative functional genomics.
doi:10.3389/fgene.2014.00264
PMCID: PMC4123725  PMID: 25147557
functional annotation; Gene Ontology annotation; annotation pipeline; manual annotation; electronic annotation
3.  Heterochromatic sequences in a Drosophila whole-genome shotgun assembly 
Genome Biology  2002;3(12):research0085.1-85.16.
Annotation of an improved whole-genome shotgun assembly of the Drosophila melanogaster genome predicted 297 protein-coding genes and six non-protein-coding genes, including known heterochromatic genes, and regions of similarity to known transposable elements. Fluorescence in situ hybridization was used to correlate the genomic sequence with the cytogenetic map; the annotated euchromatic sequence extends into the centric heterochromatin on each chromosome arm.
Background
Most eukaryotic genomes include a substantial repeat-rich fraction termed heterochromatin, which is concentrated in centric and telomeric regions. The repetitive nature of heterochromatic sequence makes it difficult to assemble and analyze. To better understand the heterochromatic component of the Drosophila melanogaster genome, we characterized and annotated portions of a whole-genome shotgun sequence assembly.
Results
WGS3, an improved whole-genome shotgun assembly, includes 20.7 Mb of draft-quality sequence not represented in the Release 3 sequence spanning the euchromatin. We annotated this sequence using the methods employed in the re-annotation of the Release 3 euchromatic sequence. This analysis predicted 297 protein-coding genes and six non-protein-coding genes, including known heterochromatic genes, and regions of similarity to known transposable elements. Bacterial artificial chromosome (BAC)-based fluorescence in situ hybridization analysis was used to correlate the genomic sequence with the cytogenetic map in order to refine the genomic definition of the centric heterochromatin; on the basis of our cytological definition, the annotated Release 3 euchromatic sequence extends into the centric heterochromatin on each chromosome arm.
Conclusions
Whole-genome shotgun assembly produced a reliable draft-quality sequence of a significant part of the Drosophila heterochromatin. Annotation of this sequence defined the intron-exon structures of 30 known protein-coding genes and 267 protein-coding gene models. The cytogenetic mapping suggests that an additional 150 predicted genes are located in heterochromatin at the base of the Release 3 euchromatic sequence. Our analysis suggests strategies for improving the sequence and annotation of the heterochromatic portions of the Drosophila and other complex genomes.
doi:10.1186/gb-2002-3-12-research0085
PMCID: PMC151187  PMID: 12537574
4.  A Drosophila full-length cDNA resource 
Genome Biology  2002;3(12):research0080.1-80.8.
High-quality full-insert sequence for 8,921 putative full-length cDNA clones in the Drosophila Gene Collection has been generated and compared to the annotated Release 3 genomic sequence. More than 5,300 cDNAs have been identifieed that contain a complete and accurate protein-coding sequence, corresponding to at least one splice form for 40% of the predicted D. melanogaster genes.
Background
A collection of sequenced full-length cDNAs is an important resource both for functional genomics studies and for the determination of the intron-exon structure of genes. Providing this resource to the Drosophila melanogaster research community has been a long-term goal of the Berkeley Drosophila Genome Project. We have previously described the Drosophila Gene Collection (DGC), a set of putative full-length cDNAs that was produced by generating and analyzing over 250,000 expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages.
Results
We have generated high-quality full-insert sequence for 8,921 clones in the DGC. We compared the sequence of these clones to the annotated Release 3 genomic sequence, and identified more than 5,300 cDNAs that contain a complete and accurate protein-coding sequence. This corresponds to at least one splice form for 40% of the predicted D. melanogaster genes. We also identified potential new cases of RNA editing.
Conclusions
We show that comparison of cDNA sequences to a high-quality annotated genomic sequence is an effective approach to identifying and eliminating defective clones from a cDNA collection and ensure its utility for experimentation. Clones were eliminated either because they carry single nucleotide discrepancies, which most probably result from reverse transcriptase errors, or because they are truncated and contain only part of the protein-coding sequence.
doi:10.1186/gb-2002-3-12-research0080
PMCID: PMC151182  PMID: 12537569
5.  The FlyBase database of the Drosophila genome projects and community literature 
Nucleic Acids Research  2003;31(1):172-175.
FlyBase (http://flybase.bio.indiana.edu/) provides an integrated view of the fundamental genomic and genetic data on the major genetic model Drosophila melanogaster and related species. FlyBase has primary responsibility for the continual reannotation of the D. melanogaster genome. The ultimate goal of the reannotation effort is to decorate the euchromatic sequence of the genome with as much biological information as is available from the community and from the major genome project centers. A complete revision of the annotations of the now-finished euchromatic genomic sequence has been completed. There are many points of entry to the genome within FlyBase, most notably through maps, gene products and ontologies, structured phenotypic and gene expression data, and anatomy.
PMCID: PMC165541  PMID: 12519974
6.  EGASP: the human ENCODE Genome Annotation Assessment Project 
Genome Biology  2006;7(Suppl 1):S2.
Background
We present the results of EGASP, a community experiment to assess the state-of-the-art in genome annotation within the ENCODE regions, which span 1% of the human genome sequence. The experiment had two major goals: the assessment of the accuracy of computational methods to predict protein coding genes; and the overall assessment of the completeness of the current human genome annotations as represented in the ENCODE regions. For the computational prediction assessment, eighteen groups contributed gene predictions. We evaluated these submissions against each other based on a 'reference set' of annotations generated as part of the GENCODE project. These annotations were not available to the prediction groups prior to the submission deadline, so that their predictions were blind and an external advisory committee could perform a fair assessment.
Results
The best methods had at least one gene transcript correctly predicted for close to 70% of the annotated genes. Nevertheless, the multiple transcript accuracy, taking into account alternative splicing, reached only approximately 40% to 50% accuracy. At the coding nucleotide level, the best programs reached an accuracy of 90% in both sensitivity and specificity. Programs relying on mRNA and protein sequences were the most accurate in reproducing the manually curated annotations. Experimental validation shows that only a very small percentage (3.2%) of the selected 221 computationally predicted exons outside of the existing annotation could be verified.
Conclusion
This is the first such experiment in human DNA, and we have followed the standards established in a similar experiment, GASP1, in Drosophila melanogaster. We believe the results presented here contribute to the value of ongoing large-scale annotation projects and should guide further experimental methods when being scaled up to the entire human genome sequence.
doi:10.1186/gb-2006-7-s1-s2
PMCID: PMC1810551  PMID: 16925836
7.  The FlyBase database of the Drosophila genome projects and community literature 
Nucleic Acids Research  2002;30(1):106-108.
FlyBase (http://flybase.bio.indiana.edu/) provides an integrated view of the fundamental genomic and genetic data on the major genetic model Drosophila melanogaster and related species. Following on the success of the Drosophila genome project, FlyBase has primary responsibility for the continual reannotation of the D.melanogaster genome. The ultimate goal of the reannotation effort is to decorate the euchromatic sequence of the genome with as much biological information as is available from the community and from the major genome project centers. The current cycle of reannotation focuses on establishing a comprehensive data set of gene models (i.e. transcription units and CDSs). There are many points of entry to the genome within FlyBase, most notably through maps, gene ontologies, structured phenotypic and gene expression data, and anatomy.
PMCID: PMC99082  PMID: 11752267
8.  Apollo: a sequence annotation editor 
Genome Biology  2002;3(12):research0082.1-82.14.
Apollo was developed to enable curators to inspect genome annotations closely and edit them. FlyBase biologists successfully used Apollo to annotate the Drosophila melanogaster genome.
The well-established inaccuracy of purely computational methods for annotating genome sequences necessitates an interactive tool to allow biological experts to refine these approximations by viewing and independently evaluating the data supporting each annotation. Apollo was developed to meet this need, enabling curators to inspect genome annotations closely and edit them. FlyBase biologists successfully used Apollo to annotate the Drosophila melanogaster genome and it is increasingly being used as a starting point for the development of customized annotation editing tools for other genome projects.
doi:10.1186/gb-2002-3-12-research0082
PMCID: PMC151184  PMID: 12537571
9.  Prediction of Gene Expression in Embryonic Structures of Drosophila melanogaster 
PLoS Computational Biology  2007;3(7):e144.
Understanding how sets of genes are coordinately regulated in space and time to generate the diversity of cell types that characterise complex metazoans is a major challenge in modern biology. The use of high-throughput approaches, such as large-scale in situ hybridisation and genome-wide expression profiling via DNA microarrays, is beginning to provide insights into the complexities of development. However, in many organisms the collection and annotation of comprehensive in situ localisation data is a difficult and time-consuming task. Here, we present a widely applicable computational approach, integrating developmental time-course microarray data with annotated in situ hybridisation studies, that facilitates the de novo prediction of tissue-specific expression for genes that have no in vivo gene expression localisation data available. Using a classification approach, trained with data from microarray and in situ hybridisation studies of gene expression during Drosophila embryonic development, we made a set of predictions on the tissue-specific expression of Drosophila genes that have not been systematically characterised by in situ hybridisation experiments. The reliability of our predictions is confirmed by literature-derived annotations in FlyBase, by overrepresentation of Gene Ontology biological process annotations, and, in a selected set, by detailed gene-specific studies from the literature. Our novel organism-independent method will be of considerable utility in enriching the annotation of gene function and expression in complex multicellular organisms.
Author Summary
The task of deciphering the complex transcriptional regulatory networks controlling development is one of the major current challenges for molecular biology. The problem is difficult, if not impossible, to solve without a detailed knowledge of the spatiotemporal dynamics of gene expression. Thus, to understand development, we need to identify and functionally characterize all players in regulatory networks. Data on gene expression dynamics obtained from whole transcriptome microarray experiments, combined with in situ hybridization mRNA localisation patterns for a subset of genes, may provide a route for predicting the localisation of gene expression for those genes for which in situ data has not been generated, as well as suggesting functional information for uncharacterised genes. Here, we report the development of one of the first methods for predicting the localisation of gene expression during Drosophila embryogenesis from microarray data. Pooling the subset of genes in the fly genome with in situ data to form functional units, localised in space and time for relevant developmental processes, facilitates the statement of a classification problem, which we address with machine-learning methods. Our approach promotes a richer annotation of biological function for genes in the absence of costly and time-consuming experimental analysis.
doi:10.1371/journal.pcbi.0030144
PMCID: PMC1924873  PMID: 17658945
10.  Evolutionary Modeling and Prediction of Non-Coding RNAs in Drosophila 
PLoS ONE  2009;4(8):e6478.
We performed benchmarks of phylogenetic grammar-based ncRNA gene prediction, experimenting with eight different models of structural evolution and two different programs for genome alignment. We evaluated our models using alignments of twelve Drosophila genomes. We find that ncRNA prediction performance can vary greatly between different gene predictors and subfamilies of ncRNA gene. Our estimates for false positive rates are based on simulations which preserve local islands of conservation; using these simulations, we predict a higher rate of false positives than previous computational ncRNA screens have reported. Using one of the tested prediction grammars, we provide an updated set of ncRNA predictions for D. melanogaster and compare them to previously-published predictions and experimental data. Many of our predictions show correlations with protein-coding genes. We found significant depletion of intergenic predictions near the 3′ end of coding regions and furthermore depletion of predictions in the first intron of protein-coding genes. Some of our predictions are colocated with larger putative unannotated genes: for example, 17 of our predictions showing homology to the RFAM family snoR28 appear in a tandem array on the X chromosome; the 4.5 Kbp spanned by the predicted tandem array is contained within a FlyBase-annotated cDNA.
doi:10.1371/journal.pone.0006478
PMCID: PMC2721679  PMID: 19668382
11.  FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database 
Nucleic Acids Research  2009;38(Database issue):D443-D447.
FlyTF (http://www.flytf.org) is a database of computationally predicted and/or experimentally verified site-specific transcription factors (TFs) in the fruit fly Drosophila melanogaster. The manual classification of TFs in the initial version of FlyTF that concentrated primarily on the DNA-binding characteristics of the proteins has now been extended to a more fine-grained annotation of both DNA binding and regulatory properties in the new release. Furthermore, experimental evidence from the literature was classified into a defined vocabulary, and in collaboration with FlyBase, translated into Gene Ontology (GO) annotation. While our GO annotations will also be available through FlyBase as they will be incorporated into the genes’ official GO annotation in the future, the entire evidence used for classification including computational predictions and quotes from the literature can be accessed through FlyTF. The FlyTF website now builds upon the InterMine framework, which provides experimental and computational biologists with powerful search and filter functionality, list management tools and access to genomic information associated with the TFs.
doi:10.1093/nar/gkp910
PMCID: PMC2808907  PMID: 19884132
12.  Characterization of 954 bovine full-CDS cDNA sequences 
BMC Genomics  2005;6:166.
Background
Genome assemblies rely on the existence of transcript sequence to stitch together contigs, verify assembly of whole genome shotgun reads, and annotate genes. Functional genomics studies also rely on transcript sequence to create expression microarrays or interpret digital tag data produced by methods such as Serial Analysis of Gene Expression (SAGE). Transcript sequence can be predicted based on reconstruction from overlapping expressed sequence tags (EST) that are obtained by single-pass sequencing of random cDNA clones, but these reconstructions are prone to errors caused by alternative splice forms, transcripts from gene families with related sequences, and expressed pseudogenes. These errors confound genome assembly and annotation. The most useful transcript sequences are derived by complete insert sequencing of clones containing the entire length, or at least the full protein coding sequence (CDS) portion, of the source mRNA. While the bovine genome sequencing initiative is nearing completion, there is currently a paucity of bovine full-CDS mRNA and protein sequence data to support bovine genome assembly and functional genomics studies. Consequently, the production of high-quality bovine full-CDS cDNA sequences will enhance the bovine genome assembly and functional studies of bovine genes and gene products. The goal of this investigation was to identify and characterize the full-CDS sequences of bovine transcripts from clones identified in non-full-length enriched cDNA libraries. In contrast to several recent full-length cDNA investigations, these full-CDS cDNAs were selected, sequenced, and annotated without the benefit of the target organism's genomic sequence, by using comparison of bovine EST sequence to existing human mRNA to identify likely full-CDS clones for full-length insert cDNA (FLIC) sequencing.
Results
The predicted bovine protein lengths, 5' UTR lengths, and Kozak consensus sequences from 954 bovine FLIC sequences (bFLICs; average length 1713 nt, representing 762 distinct loci) are all consistent with previously sequenced mammalian full-length transcripts.
Conclusion
In most cases, the bFLICs span the entire CDS of the genes, providing the basis for creating predicted bovine protein sequences to support proteomics and comparative evolutionary research as well as functional genomics and genome annotation. The results demonstrate the utility of the comparative approach in obtaining predicted protein sequences in other species.
doi:10.1186/1471-2164-6-166
PMCID: PMC1314900  PMID: 16305752
13.  An integrated gene annotation and transcriptional profiling approach towards the full gene content of the Drosophila genome 
Genome Biology  2003;5(1):R3.
A novel Drosophila microarray constructed on the basis of an integrated in silico/wet biology approach provides evidence for the transcription of approximately 2,600 additional genes. Validation indicates a lower limit of 2,000 novel annotations, thus raising the number of genes that make a fly.
Background
While the genome sequences for a variety of organisms are now available, the precise number of the genes encoded is still a matter of debate. For the human genome several stringent annotation approaches have resulted in the same number of potential genes, but a careful comparison revealed only limited overlap. This indicates that only the combination of different computational prediction methods and experimental evaluation of such in silico data will provide more complete genome annotations. In order to get a more complete gene content of the Drosophila melanogaster genome, we based our new D. melanogaster whole-transcriptome microarray, the Heidelberg FlyArray, on the combination of the Berkeley Drosophila Genome Project (BDGP) annotation and a novel ab initio gene prediction of lower stringency using the Fgenesh software.
Results
Here we provide evidence for the transcription of approximately 2,600 additional genes predicted by Fgenesh. Validation of the developmental profiling data by RT-PCR and in situ hybridization indicates a lower limit of 2,000 novel annotations, thus substantially raising the number of genes that make a fly.
Conclusions
The successful design and application of this novel Drosophila microarray on the basis of our integrated in silico/wet biology approach confirms our expectation that in silico approaches alone will always tend to be incomplete. The identification of at least 2,000 novel genes highlights the importance of gathering experimental evidence to discover all genes within a genome. Moreover, as such an approach is independent of homology criteria, it will allow the discovery of novel genes unrelated to known protein families or those that have not been strictly conserved between species.
doi:10.1186/gb-2003-5-1-r3
PMCID: PMC395735  PMID: 14709175
14.  Analysis of 14 BAC sequences from the Aedes aegypti genome: a benchmark for genome annotation and assembly 
Genome Biology  2007;8(5):R88.
In order to provide a set of manually curated and annotated sequences from the Aedes aegypti genome, mapped BAC clones encompassing 1.57 Mb were sequenced, assembled and manually annotated using computational gene-finding, EST matches as well as comparative protein homology.
Background
Aedes aegypti is the principal vector of yellow fever and dengue viruses throughout the tropical world. To provide a set of manually curated and annotated sequences from the Ae. aegypti genome, 14 mapped bacterial artificial chromosome (BAC) clones encompassing 1.57 Mb were sequenced, assembled and manually annotated using a combination of computational gene-finding, expressed sequence tag (EST) matches and comparative protein homology. PCR and sequencing were used to experimentally confirm expression and sequence of a subset of these transcripts.
Results
Of the 51 manual annotations, 50 and 43 demonstrated a high level of similarity to Anopheles gambiae and Drosophila melanogaster genes, respectively. Ten of the 12 BAC sequences with more than one annotated gene exhibited synteny with the A. gambiae genome. Putative transcripts from eight BAC clones were found in multiple copies (two copies in most cases) in the Aedes genome assembly, which point to the probable presence of haplotype polymorphisms and/or misassemblies.
Conclusion
This study not only provides a benchmark set of manually annotated transcripts for this genome that can be used to assess the quality of the auto-annotation pipeline and the assembly, but it also looks at the effect of a high repeat content on the genome assembly and annotation pipeline.
doi:10.1186/gb-2007-8-5-r88
PMCID: PMC1929151  PMID: 17519023
15.  MitoDrome: a database of Drosophila melanogaster nuclear genes encoding proteins targeted to the mitochondrion 
Nucleic Acids Research  2003;31(1):322-324.
Mitochondria are organelles present in the cytoplasm of most eukaryotic cells; although they have their own DNA, the majority of the proteins necessary for a functional mitochondrion are coded by the nuclear DNA and only after transcription and translation they are imported in the mitochondrion as proteins. The primary role of the mitochondrion is electron transport and oxidative phosphorylation. Although it has been studied for a long time, the interest of researchers in mitochondria is still alive thanks to the discovery of mitochondrial role in apoptosis, aging and cancer. Aim of the MitoDrome database is to annotate the Drosophila melanogaster nuclear genes coding for mitochondrial proteins in order to contribute to the functional characterization of nuclear genes coding for mitochondrial proteins and to knowledge of gene diseases related to mitochondrial dysfunctions. Indeed D. melanogaster is one of the most studied organisms and a model for the Human genome. Data are derived from the comparison of Human mitochondrial proteins versus the Drosophila genome, ESTs and cDNA sequence data available in the FlyBase database. Links from the MitoDrome entries to the related homologous entries available in MitoNuC will be soon imple-mented. The MitoDrome database is available at http://bighost.area.ba.cnr.it/BIG/MitoDrome. Data are organised in a flat-file format and can be retrieved using the SRS system.
PMCID: PMC165570  PMID: 12520013
16.  Gene models from ESTs (GeneModelEST): an application on the Solanum lycopersicum genome 
BMC Bioinformatics  2007;8(Suppl 1):S9.
Background
The structure annotation of a genome is based either on ab initio methodologies or on similaritiy searches versus molecules that have been already annotated. Ab initio gene predictions in a genome are based on a priori knowledge of species-specific features of genes. The training of ab initio gene finders is based on the definition of a data-set of gene models. To accomplish this task the common approach is to align species-specific full length cDNA and EST sequences along the genomic sequences in order to define exon/intron structure of mRNA coding genes.
Results
GeneModelEST is the software here proposed for defining a data-set of candidate gene models using exclusively evidence derived from cDNA/EST sequences.
GeneModelEST requires the genome coordinates of the spliced-alignments of ESTs and of contigs (tentative consensus sequences) generated by an EST clustering/assembling procedure to be formatted in a General Feature Format (GFF) standard file. Moreover, the alignments of the contigs versus a protein database are required as an NCBI BLAST formatted report file.
The GeneModelEST analysis aims to i) evaluate each exon as defined from contig spliced alignments onto the genome sequence; ii) classify the contigs according to quality levels in order to select candidate gene models; iii) assign to the candidate gene models preliminary functional annotations.
We discuss the application of the proposed methodology to build a data-set of gene models of Solanum lycopersicum, whose genome sequencing is an ongoing effort by the International Tomato Genome Sequencing Consortium.
Conclusion
The contig classification procedure used by GeneModelEST supports the detection of candidate gene models, the identification of potential alternative transcripts and it is useful to filter out ambiguous information. An automated procedure, such as the one proposed here, is fundamental to support large scale analysis in order to provide species-specific gene models, that could be useful as a training data-set for ab initio gene finders and/or as a reference gene list for a human curated annotation.
doi:10.1186/1471-2105-8-S1-S9
PMCID: PMC1885861  PMID: 17430576
17.  tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles 
The breadth and depth of biomedical literature are increasing year upon year. To keep abreast of these increases, FlyBase, a database for Drosophila genomic and genetic information, is constantly exploring new ways to mine the published literature to increase the efficiency and accuracy of manual curation and to automate some aspects, such as triaging and entity extraction. Toward this end, we present the ‘tagtog’ system, a web-based annotation framework that can be used to mark up biological entities (such as genes) and concepts (such as Gene Ontology terms) in full-text articles. tagtog leverages manual user annotation in combination with automatic machine-learned annotation to provide accurate identification of gene symbols and gene names. As part of the BioCreative IV Interactive Annotation Task, FlyBase has used tagtog to identify and extract mentions of Drosophila melanogaster gene symbols and names in full-text biomedical articles from the PLOS stable of journals. We show here the results of three experiments with different sized corpora and assess gene recognition performance and curation speed. We conclude that tagtog-named entity recognition improves with a larger corpus and that tagtog-assisted curation is quicker than manual curation.
Database URL: www.tagtog.net, www.flybase.org
doi:10.1093/database/bau033
PMCID: PMC3978375  PMID: 24715220
18.  Automatic categorization of diverse experimental information in the bioscience literature 
BMC Bioinformatics  2012;13:16.
Background
Curation of information from bioscience literature into biological knowledge databases is a crucial way of capturing experimental information in a computable form. During the biocuration process, a critical first step is to identify from all published literature the papers that contain results for a specific data type the curator is interested in annotating. This step normally requires curators to manually examine many papers to ascertain which few contain information of interest and thus, is usually time consuming. We developed an automatic method for identifying papers containing these curation data types among a large pool of published scientific papers based on the machine learning method Support Vector Machine (SVM). This classification system is completely automatic and can be readily applied to diverse experimental data types. It has been in use in production for automatic categorization of 10 different experimental datatypes in the biocuration process at WormBase for the past two years and it is in the process of being adopted in the biocuration process at FlyBase and the Saccharomyces Genome Database (SGD). We anticipate that this method can be readily adopted by various databases in the biocuration community and thereby greatly reducing time spent on an otherwise laborious and demanding task. We also developed a simple, readily automated procedure to utilize training papers of similar data types from different bodies of literature such as C. elegans and D. melanogaster to identify papers with any of these data types for a single database. This approach has great significance because for some data types, especially those of low occurrence, a single corpus often does not have enough training papers to achieve satisfactory performance.
Results
We successfully tested the method on ten data types from WormBase, fifteen data types from FlyBase and three data types from Mouse Genomics Informatics (MGI). It is being used in the curation work flow at WormBase for automatic association of newly published papers with ten data types including RNAi, antibody, phenotype, gene regulation, mutant allele sequence, gene expression, gene product interaction, overexpression phenotype, gene interaction, and gene structure correction.
Conclusions
Our methods are applicable to a variety of data types with training set containing several hundreds to a few thousand documents. It is completely automatic and, thus can be readily incorporated to different workflow at different literature-based databases. We believe that the work presented here can contribute greatly to the tremendous task of automating the important yet labor-intensive biocuration effort.
doi:10.1186/1471-2105-13-16
PMCID: PMC3305665  PMID: 22280404
19.  CAFTAN: a tool for fast mapping, and quality assessment of cDNAs 
BMC Bioinformatics  2006;7:473.
Background
The German cDNA Consortium has been cloning full length cDNAs and continued with their exploitation in protein localization experiments and cellular assays. However, the efficient use of large cDNA resources requires the development of strategies that are capable of a speedy selection of truly useful cDNAs from biological and experimental noise. To this end we have developed a new high-throughput analysis tool, CAFTAN, which simplifies these efforts and thus fills the gap between large-scale cDNA collections and their systematic annotation and application in functional genomics.
Results
CAFTAN is built around the mapping of cDNAs to the genome assembly, and the subsequent analysis of their genomic context. It uses sequence features like the presence and type of PolyA signals, inner and flanking repeats, the GC-content, splice site types, etc. All these features are evaluated in individual tests and classify cDNAs according to their sequence quality and likelihood to have been generated from fully processed mRNAs. Additionally, CAFTAN compares the coordinates of mapped cDNAs with the genomic coordinates of reference sets from public available resources (e.g., VEGA, ENSEMBL). This provides detailed information about overlapping exons and the structural classification of cDNAs with respect to the reference set of splice variants.
The evaluation of CAFTAN showed that is able to correctly classify more than 85% of 5950 selected "known protein-coding" VEGA cDNAs as high quality multi- or single-exon. It identified as good 80.6 % of the single exon cDNAs and 85 % of the multiple exon cDNAs.
The program is written in Perl and in a modular way, allowing the adoption of this strategy to other tasks like EST-annotation, or to extend it by adding new classification rules and new organism databases as they become available. We think that it is a very useful program for the annotation and research of unfinished genomes.
Conclusion
CAFTAN is a high-throughput sequence analysis tool, which performs a fast and reliable quality prediction of cDNAs. Several thousands of cDNAs can be analyzed in a short time, giving the curator/scientist a first quick overview about the quality and the already existing annotation of a set of cDNAs. It supports the rejection of low quality cDNAs and helps in the selection of likely novel splice variants, and/or completely novel transcripts for new experiments.
doi:10.1186/1471-2105-7-473
PMCID: PMC1636072  PMID: 17064411
20.  FlyBase: anatomical data, images and queries 
Nucleic Acids Research  2005;34(Database issue):D484-D488.
FlyBase () is a database of genetic and genomic data on the model organism Drosophila melanogaster and the entire insect family Drosophilidae. The FlyBase Consortium curates, annotates, integrates and maintains a wide variety of data within this domain. Access to the data is provided through graphical and textual user interfaces tailored to particular types of data. FlyBase data types include maps at the cytological, genetic and sequence levels, genes and alleles including their products, functions, expression patterns, mutant phenotypes and genetic interactions as well as aberrant chromosomes, annotated genomes, genetic stock collections, transposons, transgene constructs and insertions, anatomy and images, bibliographic data, and community contact information.
doi:10.1093/nar/gkj068
PMCID: PMC1347431  PMID: 16381917
21.  Identification of unannotated exons of low abundance transcripts in Drosophila melanogaster and cloning of a new serine protease gene upregulated upon injury 
BMC Genomics  2007;8:249.
Background
The sequencing of the D.melanogaster genome revealed an unexpected small number of genes (~ 14,000) indicating that mechanisms acting on generation of transcript diversity must have played a major role in the evolution of complex metazoans. Among the most extensively used mechanisms that accounts for this diversity is alternative splicing. It is estimated that over 40% of Drosophila protein-coding genes contain one or more alternative exons. A recent transcription map of the Drosophila embryogenesis indicates that 30% of the transcribed regions are unannotated, and that 1/3 of this is estimated as missed or alternative exons of previously characterized protein-coding genes. Therefore, the identification of the variety of expressed transcripts depends on experimental data for its final validation and is continuously being performed using different approaches. We applied the Open Reading Frame Expressed Sequence Tags (ORESTES) methodology, which is capable of generating cDNA data from the central portion of rare transcripts, in order to investigate the presence of hitherto unnanotated regions of Drosophila transcriptome.
Results
Bioinformatic analysis of 1,303 Drosophila ORESTES clusters identified 68 sequences derived from unannotated regions in the current Drosophila genome version (4.3). Of these, a set of 38 was analysed by polyA+ northern blot hybridization, validating 17 (50%) new exons of low abundance transcripts. For one of these ESTs, we obtained the cDNA encompassing the complete coding sequence of a new serine protease, named SP212. The SP212 gene is part of a serine protease gene cluster located in the chromosome region 88A12-B1. This cluster includes the predicted genes CG9631, CG9649 and CG31326, which were previously identified as up-regulated after immune challenges in genomic-scale microarray analysis. In agreement with the proposal that this locus is co-regulated in response to microorganisms infection, we show here that SP212 is also up-regulated upon injury.
Conclusion
Using the ORESTES methodology we identified 17 novel exons from low abundance Drosophila transcripts, and through a PCR approach the complete CDS of one of these transcripts was defined. Our results show that the computational identification and manual inspection are not sufficient to annotate a genome in the absence of experimentally derived data.
doi:10.1186/1471-2164-8-249
PMCID: PMC1949825  PMID: 17650329
22.  Ab Initio Prediction of Transcription Factor Targets Using Structural Knowledge 
Current approaches for identification and detection of transcription factor binding sites rely on an extensive set of known target genes. Here we describe a novel structure-based approach applicable to transcription factors with no prior binding data. Our approach combines sequence data and structural information to infer context-specific amino acid–nucleotide recognition preferences. These are used to predict binding sites for novel transcription factors from the same structural family. We demonstrate our approach on the Cys2His2 Zinc Finger protein family, and show that the learned DNA-recognition preferences are compatible with experimental results. We use these preferences to perform a genome-wide scan for direct targets of Drosophila melanogaster Cys2His2 transcription factors. By analyzing the predicted targets along with gene annotation and expression data we infer the function and activity of these proteins.
Synopsis
Cells respond to dynamic changes in their environment by invoking various cellular processes, coordinated by a complex regulatory program. A main component of this program is the regulation of transcription, which is mainly accomplished by transcription factors that bind the DNA in the vicinity of genes. To better understand transcriptional regulation, advanced computational approaches are needed for linking between transcription factors and their targets. The authors describe a novel approach by which the binding site of a given transcription factor can be characterized without previous experimental binding data. This approach involves learning a set of context-specific amino acid–nucleotide recognition preferences that, when combined with the sequence and structure of the protein, can predict its specific binding preferences. Applying this approach to the Cys2His2 Zinc Finger protein family demonstrated its genome-wide potential by automatically predicting the direct targets of 29 regulators in the genome of the fruit fly Drosophila melanogaster. At present, with the availability of many genome sequences, there are numerous proteins annotated as transcription factors based on their sequence alone. This approach offers a promising direction for revealing the targets of these factors and for understanding their roles in the cellular network.
doi:10.1371/journal.pcbi.0010001
PMCID: PMC1183507  PMID: 16103898
23.  A Machine Learning Approach for Identifying Novel Cell Type–Specific Transcriptional Regulators of Myogenesis 
PLoS Genetics  2012;8(3):e1002531.
Transcriptional enhancers integrate the contributions of multiple classes of transcription factors (TFs) to orchestrate the myriad spatio-temporal gene expression programs that occur during development. A molecular understanding of enhancers with similar activities requires the identification of both their unique and their shared sequence features. To address this problem, we combined phylogenetic profiling with a DNA–based enhancer sequence classifier that analyzes the TF binding sites (TFBSs) governing the transcription of a co-expressed gene set. We first assembled a small number of enhancers that are active in Drosophila melanogaster muscle founder cells (FCs) and other mesodermal cell types. Using phylogenetic profiling, we increased the number of enhancers by incorporating orthologous but divergent sequences from other Drosophila species. Functional assays revealed that the diverged enhancer orthologs were active in largely similar patterns as their D. melanogaster counterparts, although there was extensive evolutionary shuffling of known TFBSs. We then built and trained a classifier using this enhancer set and identified additional related enhancers based on the presence or absence of known and putative TFBSs. Predicted FC enhancers were over-represented in proximity to known FC genes; and many of the TFBSs learned by the classifier were found to be critical for enhancer activity, including POU homeodomain, Myb, Ets, Forkhead, and T-box motifs. Empirical testing also revealed that the T-box TF encoded by org-1 is a previously uncharacterized regulator of muscle cell identity. Finally, we found extensive diversity in the composition of TFBSs within known FC enhancers, suggesting that motif combinatorics plays an essential role in the cellular specificity exhibited by such enhancers. In summary, machine learning combined with evolutionary sequence analysis is useful for recognizing novel TFBSs and for facilitating the identification of cognate TFs that coordinate cell type–specific developmental gene expression patterns.
Author Summary
The development of multicellular organisms requires the formation of a diversity of cell types. Each cell has a unique genetic program that is orchestrated by regulatory sequences called enhancers, comprising multiple short DNA sequences that bind distinct transcription factors. Understanding developmental regulatory networks requires knowledge of the sequence features of functionally related enhancers. We developed an integrated evolutionary and computational approach for deciphering enhancer regulatory codes and applied this method to discover new components of the transcriptional network controlling muscle development in the fruit fly, Drosophila melanogaster. Our method involves assembling known muscle enhancers, expanding this set with evolutionarily conserved sequences, computationally classifying these enhancers based on their shared sequence features, and scanning the entire Drosophila genome to predict additional related enhancers. Using this approach, we created a map of 5,500 putative muscle enhancers, identified candidate transcription factors to which they bind, observed a strong correlation between mapped enhancers and muscle gene expression, and uncovered extensive heterogeneity among combinations of transcription factor binding sites in validated muscle enhancers, a feature that may contribute to the individual cellular specificities of these regulatory elements. Our strategy can readily be generalized to study transcriptional networks in other organisms and developmental contexts.
doi:10.1371/journal.pgen.1002531
PMCID: PMC3297574  PMID: 22412381
24.  FlyPhy: a phylogenomic analysis platform for Drosophila genes and gene families 
BMC Bioinformatics  2009;10:123.
Background
The availability of 12 fully sequenced Drosophila species genomes provides an excellent opportunity to explore the evolutionary mechanism, structure and function of gene families in Drosophila. Currently, several important resources, such as FlyBase, FlyMine and DroSpeGe, have been devoted to integrating genetic, genomic, and functional data of Drosophila into a well-organized form. However, all of these resources are gene-centric and lack the information of the gene families in Drosophila.
Description
FlyPhy is a comprehensive phylogenomic analysis platform devoted to analyzing the genes and gene families in Drosophila. Genes were classified into families using a graph-based Markov Clustering algorithm and extensively annotated by a number of bioinformatic tools, such as basic sequence features, functional category, gene ontology terms, domain organization and sequence homolog to other databases. FlyPhy provides a simple and user-friendly web interface to allow users to browse and retrieve the information at multiple levels. An outstanding feature of the FlyPhy is that all the retrieved results can be added to a workset for further data manipulation. For the data stored in the workset, multiple sequence alignment, phylogenetic tree construction and visualization can be easily performed to investigate the sequence variation of each given family and to explore its evolutionary mechanism.
Conclusion
With the above functionalities, FlyPhy will be a useful resource and convenient platform for the Drosophila research community. The FlyPhy is available at .
doi:10.1186/1471-2105-10-123
PMCID: PMC2680407  PMID: 19393099
25.  Identification of Drosophila MicroRNA Targets 
PLoS Biology  2003;1(3):e60.
MicroRNAs (miRNAs) are short RNA molecules that regulate gene expression by binding to target messenger RNAs and by controlling protein production or causing RNA cleavage. To date, functions have been assigned to only a few of the hundreds of identified miRNAs, in part because of the difficulty in identifying their targets. The short length of miRNAs and the fact that their complementarity to target sequences is imperfect mean that target identification in animal genomes is not possible by standard sequence comparison methods. Here we screen conserved 3′ UTR sequences from the Drosophila melanogaster genome for potential miRNA targets. The screening procedure combines a sequence search with an evaluation of the predicted miRNA–target heteroduplex structures and energies. We show that this approach successfully identifies the five previously validated let-7, lin-4, and bantam targets from a large database and predict new targets for Drosophila miRNAs. Our target predictions reveal striking clusters of functionally related targets among the top predictions for specific miRNAs. These include Notch target genes for miR-7, proapoptotic genes for the miR-2 family, and enzymes from a metabolic pathway for miR-277. We experimentally verified three predicted targets each for miR-7 and the miR-2 family, doubling the number of validated targets for animal miRNAs. Statistical analysis indicates that the best single predicted target sites are at the border of significance; thus, target predictions should be considered as tentative until experimentally validated. We identify features shared by all validated targets that can be used to evaluate target predictions for animal miRNAs. Our initial evaluation and experimental validation of target predictions suggest functions for two miRNAs. For others, the screen suggests plausible functions, such as a role for miR-277 as a metabolic switch controlling amino acid catabolism. Cross-genome comparison proved essential, as it allows reduction of the sequence search space. Improvements in genome annotation and increased availability of cDNA sequences from other genomes will allow more sensitive screens. An increase in the number of confirmed targets is expected to reveal general structural features that can be used to improve their detection. While the screen is likely to miss some targets, our study shows that valid targets can be identified from sequence alone.
A bioinformatic approach suggests many new target genes for Drosophila microRNAs. A number of them are validated experimentally
doi:10.1371/journal.pbio.0000060
PMCID: PMC270017  PMID: 14691535

Results 1-25 (964411)