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1.  ProTISA: a comprehensive resource for translation initiation site annotation in prokaryotic genomes 
Nucleic Acids Research  2007;36(Database issue):D114-D119.
Correct annotation of translation initiation site (TIS) is essential for both experiments and bioinformatics studies of prokaryotic translation initiation mechanism as well as understanding of gene regulation and gene structure. Here we describe a comprehensive database ProTISA, which collects TIS confirmed through a variety of available evidences for prokaryotic genomes, including Swiss-Prot experiments record, literature, conserved domain hits and sequence alignment between orthologous genes. Moreover, by combining the predictions from our recently developed TIS post-processor, ProTISA provides a refined annotation for the public database RefSeq. Furthermore, the database annotates the potential regulatory signals associated with translation initiation at the TIS upstream region. As of July 2007, ProTISA includes 440 microbial genomes with more than 390 000 confirmed TISs. The database is available at
PMCID: PMC2238952  PMID: 17942412
2.  DIGAP - a Database of Improved Gene Annotation for Phytopathogens 
BMC Genomics  2010;11:54.
Bacterial plant pathogens are very harmful to their host plants, which can cause devastating agricultural losses in the world. With the development of microbial genome sequencing, many strains of phytopathogens have been sequenced. However, some misannotations exist in these phytopathogen genomes. Our objective is to improve these annotations and store them in a central database DIGAP.
DIGAP includes the following improved information on phytopathogen genomes. (i) All the 'hypothetical proteins' were checked, and non-coding ORFs recognized by the Z curve method were removed. (ii) The translation initiation sites (TISs) of 20% ~ 25% of all the protein-coding genes have been corrected based on the NCBI RefSeq, ProTISA database and an ab initio program, GS-Finder. (iii) Potential functions of about 10% 'hypothetical proteins' have been predicted using sequence alignment tools. (iv) Two theoretical gene expression indices, the codon adaptation index (CAI) and the E(g) index, were calculated to predict the gene expression levels. (v) Potential agricultural bactericide targets and their homology-modeled 3D structures are provided in the database, which is of significance for agricultural antibiotic discovery.
The results in DIGAP provide useful information for understanding the pathogenetic mechanisms of phytopathogens and for finding agricultural bactericides. DIGAP is freely available at
PMCID: PMC2825234  PMID: 20089203
3.  Genome reannotation of Escherichia coli CFT073 with new insights into virulence 
BMC Genomics  2009;10:552.
As one of human pathogens, the genome of Uropathogenic Escherichia coli strain CFT073 was sequenced and published in 2002, which was significant in pathogenetic bacterial genomics research. However, the current RefSeq annotation of this pathogen is now outdated to some degree, due to missing or misannotation of some essential genes associated with its virulence. We carried out a systematic reannotation by combining automated annotation tools with manual efforts to provide a comprehensive understanding of virulence for the CFT073 genome.
The reannotation excluded 608 coding sequences from the RefSeq annotation. Meanwhile, a total of 299 coding sequences were newly added, about one third of them are found in genomic island (GI) regions while more than one fifth of them are located in virulence related regions pathogenicity islands (PAIs). Furthermore, there are totally 341 genes were relocated with their translational initiation sites (TISs), which resulted in a high quality of gene start annotation. In addition, 94 pseudogenes annotated in RefSeq were thoroughly inspected and updated. The number of miscellaneous genes (sRNAs) has been updated from 6 in RefSeq to 46 in the reannotation. Based on the adjustment in the reannotation, subsequent analysis were conducted by both general and case studies on new virulence factors or new virulence-associated genes that are crucial during the urinary tract infections (UTIs) process, including invasion, colonization, nutrition uptaking and population density control. Furthermore, miscellaneous RNAs collected in the reannotation are believed to contribute to the virulence of strain CFT073. The reannotation including the nucleotide data, the original RefSeq annotation, and all reannotated results is freely available via
As a result, the reannotation presents a more comprehensive picture of mechanisms of uropathogenicity of UPEC strain CFT073. The new genes change the view of its uropathogenicity in many respects, particularly by new genes in GI regions and new virulence-associated factors. The reannotation thus functions as an important source by providing new information about genomic structure and organization, and gene function. Moreover, we expect that the detailed analysis will facilitate the studies for exploration of novel virulence mechanisms and help guide experimental design.
PMCID: PMC2785843  PMID: 19930606
4.  Comparison of RefSeq protein-coding regions in human and vertebrate genomes 
BMC Genomics  2013;14:654.
Advances in high-throughput sequencing technology have yielded a large number of publicly available vertebrate genomes, many of which are selected for inclusion in NCBI’s RefSeq project and subsequently processed by NCBI’s eukaryotic annotation pipeline. Genome annotation results are affected by differences in available support evidence and may be impacted by annotation pipeline software changes over time. The RefSeq project has not previously assessed annotation trends across organisms or over time. To address this deficiency, we have developed a comparative protocol which integrates analysis of annotated protein-coding regions across a data set of vertebrate orthologs in genomic sequence coordinates, protein sequences, and protein features.
We assessed an ortholog dataset that includes 34 annotated vertebrate RefSeq genomes including human. We confirm that RefSeq protein-coding gene annotations in mammals exhibit considerable similarity. Over 50% of the orthologous protein-coding genes in 20 organisms are supported at the level of splicing conservation with at least three selected reference genomes. Approximately 7,500 ortholog sets include at least half of the analyzed organisms, show highly similar sequence and conserved splicing, and may serve as a minimal set of mammalian “core proteins” for initial assessment of new mammalian genomes. Additionally, 80% of the proteins analyzed pass a suite of tests to detect proteins that lack splicing conservation and have unusual sequence or domain annotation. We use these tests to define an annotation quality metric that is based directly on the annotated proteins thus operates independently of other quality metrics such as availability of transcripts or assembly quality measures. Results are available on the RefSeq FTP site [].
Our multi-factored analysis demonstrates a high level of consistency in RefSeq protein representation among vertebrates. We find that the majority of the RefSeq vertebrate proteins for which we have calculated orthology are good as measured by these metrics. The process flow described provides specific information on the scope and degree of conservation for the analyzed protein sequences and annotations and will be used to enrich the quality of RefSeq records by identifying targets for further improvement in the computational annotation pipeline, and by flagging specific genes for manual curation.
PMCID: PMC3882889  PMID: 24063302
Genome annotation; RefSeq proteins; Protein quality assessment; Splice orthologs
5.  NCBI Reference Sequences: current status, policy and new initiatives 
Nucleic Acids Research  2008;37(Database issue):D32-D36.
NCBI's Reference Sequence (RefSeq) database ( is a curated non-redundant collection of sequences representing genomes, transcripts and proteins. RefSeq records integrate information from multiple sources and represent a current description of the sequence, the gene and sequence features. The database includes over 5300 organisms spanning prokaryotes, eukaryotes and viruses, with records for more than 5.5 × 106 proteins (RefSeq release 30). Feature annotation is applied by a combination of curation, collaboration, propagation from other sources and computation. We report here on the recent growth of the database, recent changes to feature annotations and record types for eukaryotic (primarily vertebrate) species and policies regarding species inclusion and genome annotation. In addition, we introduce RefSeqGene, a new initiative to support reporting variation data on a stable genomic coordinate system.
PMCID: PMC2686572  PMID: 18927115
6.  NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins 
Nucleic Acids Research  2006;35(Database issue):D61-D65.
NCBI's reference sequence (RefSeq) database () is a curated non-redundant collection of sequences representing genomes, transcripts and proteins. The database includes 3774 organisms spanning prokaryotes, eukaryotes and viruses, and has records for 2 879 860 proteins (RefSeq release 19). RefSeq records integrate information from multiple sources, when additional data are available from those sources and therefore represent a current description of the sequence and its features. Annotations include coding regions, conserved domains, tRNAs, sequence tagged sites (STS), variation, references, gene and protein product names, and database cross-references. Sequence is reviewed and features are added using a combined approach of collaboration and other input from the scientific community, prediction, propagation from GenBank and curation by NCBI staff. The format of all RefSeq records is validated, and an increasing number of tests are being applied to evaluate the quality of sequence and annotation, especially in the context of complete genomic sequence.
PMCID: PMC1716718  PMID: 17130148
7.  NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy 
Nucleic Acids Research  2011;40(Database issue):D130-D135.
The National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database is a collection of genomic, transcript and protein sequence records. These records are selected and curated from public sequence archives and represent a significant reduction in redundancy compared to the volume of data archived by the International Nucleotide Sequence Database Collaboration. The database includes over 16 000 organisms, 2.4 × 106 genomic records, 13 × 106 proteins and 2 × 106 RNA records spanning prokaryotes, eukaryotes and viruses (RefSeq release 49, September 2011). The RefSeq database is maintained by a combined approach of automated analyses, collaboration and manual curation to generate an up-to-date representation of the sequence, its features, names and cross-links to related sources of information. We report here on recent growth, the status of curating the human RefSeq data set, more extensive feature annotation and current policy for eukaryotic genome annotation via the NCBI annotation pipeline. More information about the resource is available online (see
PMCID: PMC3245008  PMID: 22121212
8.  RefSeq: an update on mammalian reference sequences 
Nucleic Acids Research  2013;42(Database issue):D756-D763.
The National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database is a collection of annotated genomic, transcript and protein sequence records derived from data in public sequence archives and from computation, curation and collaboration ( We report here on growth of the mammalian and human subsets, changes to NCBI’s eukaryotic annotation pipeline and modifications affecting transcript and protein records. Recent changes to NCBI’s eukaryotic genome annotation pipeline provide higher throughput, and the addition of RNAseq data to the pipeline results in a significant expansion of the number of transcripts and novel exons annotated on mammalian RefSeq genomes. Recent annotation changes include reporting supporting evidence for transcript records, modification of exon feature annotation and the addition of a structured report of gene and sequence attributes of biological interest. We also describe a revised protein annotation policy for alternatively spliced transcripts with more divergent predicted proteins and we summarize the current status of the RefSeqGene project.
PMCID: PMC3965018  PMID: 24259432
9.  Assessing the impact of human genome annotation choice on RNA-seq expression estimates 
BMC Bioinformatics  2013;14(Suppl 11):S8.
Genome annotation is a crucial component of RNA-seq data analysis. Much effort has been devoted to producing an accurate and rational annotation of the human genome. An annotated genome provides a comprehensive catalogue of genomic functional elements. Currently, at least six human genome annotations are publicly available, including AceView Genes, Ensembl Genes, H-InvDB Genes, RefSeq Genes, UCSC Known Genes, and Vega Genes. Characteristics of these annotations differ because of variations in annotation strategies and information sources. When performing RNA-seq data analysis, researchers need to choose a genome annotation. However, the effect of genome annotation choice on downstream RNA-seq expression estimates is still unclear. This study (1) investigates the effect of different genome annotations on RNA-seq quantification and (2) provides guidelines for choosing a genome annotation based on research focus.
We define the complexity of human genome annotations in terms of the number of genes, isoforms, and exons. This definition facilitates an investigation of potential relationships between complexity and variations in RNA-seq quantification. We apply several evaluation metrics to demonstrate the impact of genome annotation choice on RNA-seq expression estimates. In the mapping stage, the least complex genome annotation, RefSeq Genes, appears to have the highest percentage of uniquely mapped short sequence reads. In the quantification stage, RefSeq Genes results in the most stable expression estimates in terms of the average coefficient of variation over all genes. Stable expression estimates in the quantification stage translate to accurate statistics for detecting differentially expressed genes. We observe that RefSeq Genes produces the most accurate fold-change measures with respect to a ground truth of RT-qPCR gene expression estimates.
Based on the observed variations in the mapping, quantification, and differential expression calling stages, we demonstrate that the selection of human genome annotation results in different gene expression estimates. When conducting research that emphasizes reproducible and robust gene expression estimates, a less complex genome annotation may be preferred. However, simpler genome annotations may limit opportunities for identifying or characterizing novel transcriptional or regulatory mechanisms. When conducting research that aims to be more exploratory, a more complex genome annotation may be preferred.
PMCID: PMC3816316  PMID: 24564364
10.  EcoGene-RefSeq: EcoGene tools applied to the RefSeq prokaryotic genomes 
Bioinformatics  2013;29(15):1917-1918.
Summary: is a genome database and website dedicated to Escherichia coli K-12 substrain MG1655 that is revised daily using information derived from the biomedical literature and in-house analysis. EcoGene is a major source of annotation updates for the MG1655 Genbank record, one of only a few Genbank genome records that are updated by a community effort. The Reference Sequence (RefSeq) database, built by The National Center for Biotechnology Information, comprises a set of duplicate Genbank genome records that can be modified by the NCBI staff annotators. EcoGene-RefSeq is being developed as a stand-alone internet resource to facilitate the usage of EcoGene-based tools on any of the >2400 completed prokaryotic genome records that are currently available at the RefSeq database.
Availability: The web interface of EcoGene-RefSeq is available at
Contact: or
PMCID: PMC3712216  PMID: 23736533
11.  RefSeq and LocusLink: NCBI gene-centered resources 
Nucleic Acids Research  2001;29(1):137-140.
Thousands of genes have been painstakingly identified and characterized a few genes at a time. Many thousands more are being predicted by large scale cDNA and genomic sequencing projects, with levels of evidence ranging from supporting mRNA sequence and comparative genomics to computing ab initio models. This, coupled with the burgeoning scientific literature, makes it critical to have a comprehensive directory for genes and reference sequences for key genomes. The NCBI provides two resources, LocusLink and RefSeq, to meet these needs. LocusLink organizes information around genes to generate a central hub for accessing gene-specific information for fruit fly, human, mouse, rat and zebrafish. RefSeq provides reference sequence standards for genomes, transcripts and proteins; human, mouse and rat mRNA RefSeqs, and their corresponding proteins, are discussed here. Together, RefSeq and LocusLink provide a non-redundant view of genes and other loci to support research on genes and gene families, variation, gene expression and genome annotation. Additional information about LocusLink and RefSeq is available at
PMCID: PMC29787  PMID: 11125071
12.  Transcriptome sequencing of the Microarray Quality Control (MAQC) RNA reference samples using next generation sequencing 
BMC Genomics  2009;10:264.
Transcriptome sequencing using next-generation sequencing platforms will soon be competing with DNA microarray technologies for global gene expression analysis. As a preliminary evaluation of these promising technologies, we performed deep sequencing of cDNA synthesized from the Microarray Quality Control (MAQC) reference RNA samples using Roche's 454 Genome Sequencer FLX.
We generated more that 3.6 million sequence reads of average length 250 bp for the MAQC A and B samples and introduced a data analysis pipeline for translating cDNA read counts into gene expression levels. Using BLAST, 90% of the reads mapped to the human genome and 64% of the reads mapped to the RefSeq database of well annotated genes with e-values ≤ 10-20. We measured gene expression levels in the A and B samples by counting the numbers of reads that mapped to individual RefSeq genes in multiple sequencing runs to evaluate the MAQC quality metrics for reproducibility, sensitivity, specificity, and accuracy and compared the results with DNA microarrays and Quantitative RT-PCR (QRTPCR) from the MAQC studies. In addition, 88% of the reads were successfully aligned directly to the human genome using the AceView alignment programs with an average 90% sequence similarity to identify 137,899 unique exon junctions, including 22,193 new exon junctions not yet contained in the RefSeq database.
Using the MAQC metrics for evaluating the performance of gene expression platforms, the ExpressSeq results for gene expression levels showed excellent reproducibility, sensitivity, and specificity that improved systematically with increasing shotgun sequencing depth, and quantitative accuracy that was comparable to DNA microarrays and QRTPCR. In addition, a careful mapping of the reads to the genome using the AceView alignment programs shed new light on the complexity of the human transcriptome including the discovery of thousands of new splice variants.
PMCID: PMC2707382  PMID: 19523228
13.  Matching curated genome databases: a non trivial task 
BMC Genomics  2008;9:501.
Curated databases of completely sequenced genomes have been designed independently at the NCBI (RefSeq) and EBI (Genome Reviews) to cope with non-standard annotation found in the version of the sequenced genome that has been published by databanks GenBank/EMBL/DDBJ. These curation attempts were expected to review the annotations and to improve their pertinence when using them to annotate newly released genome sequences by homology to previously annotated genomes. However, we observed that such an uncoordinated effort has two unwanted consequences. First, it is not trivial to map the protein identifiers of the same sequence in both databases. Secondly, the two reannotated versions of the same genome differ at the level of their structural annotation.
Here, we propose CorBank, a program devised to provide cross-referencing protein identifiers no matter what the level of identity is found between their matching sequences. Approximately 98% of the 1,983,258 amino acid sequences are matching, allowing instantaneous retrieval of their respective cross-references. CorBank further allows detecting any differences between the independently curated versions of the same genome. We found that the RefSeq and Genome Reviews versions are perfectly matching for only 50 of the 641 complete genomes we have analyzed. In all other cases there are differences occurring at the level of the coding sequence (CDS), and/or in the total number of CDS in the respective version of the same genome.
CorBank is freely accessible at . The CorBank site contains also updated publication of the exhaustive results obtained by comparing RefSeq and Genome Reviews versions of each genome. Accordingly, this web site allows easy search of cross-references between RefSeq, Genome Reviews, and UniProt, for either a single CDS or a whole replicon.
CorBank is very efficient in rapid detection of the numerous differences existing between RefSeq and Genome Reviews versions of the same curated genome. Although such differences are acceptable as reflecting different views, we suggest that curators of both genome databases could help reducing further divergence by agreeing on a minimal dialogue and attempting to publish the point of view of the other database whenever it is technically possible.
PMCID: PMC2596144  PMID: 18950477
14.  Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut 
BMC Genomics  2014;15:37.
The main limitations in the analysis of viral metagenomes are perhaps the high genetic variability and the lack of information in extant databases. To address these issues, several bioinformatic tools have been specifically designed or adapted for metagenomics by improving read assembly and creating more sensitive methods for homology detection. This study compares the performance of different available assemblers and taxonomic annotation software using simulated viral-metagenomic data.
We simulated two 454 viral metagenomes using genomes from NCBI's RefSeq database based on the list of actual viruses found in previously published metagenomes. Three different assembly strategies, spanning six assemblers, were tested for performance: overlap-layout-consensus algorithms Newbler, Celera and Minimo; de Bruijn graphs algorithms Velvet and MetaVelvet; and read probabilistic model Genovo. The performance of the assemblies was measured by the length of resulting contigs (using N50), the percentage of reads assembled and the overall accuracy when comparing against corresponding reference genomes. Additionally, the number of chimeras per contig and the lowest common ancestor were estimated in order to assess the effect of assembling on taxonomic and functional annotation. The functional classification of the reads was evaluated by counting the reads that correctly matched the functional data previously reported for the original genomes and calculating the number of over-represented functional categories in chimeric contigs. The sensitivity and specificity of tBLASTx, PhymmBL and the k-mer frequencies were measured by accurate predictions when comparing simulated reads against the NCBI Virus genomes RefSeq database.
Assembling improves functional annotation by increasing accurate assignations and decreasing ambiguous hits between viruses and bacteria. However, the success is limited by the chimeric contigs occurring at all taxonomic levels. The assembler and its parameters should be selected based on the focus of each study. Minimo's non-chimeric contigs and Genovo's long contigs excelled in taxonomy assignation and functional annotation, respectively.
tBLASTx stood out as the best approach for taxonomic annotation for virus identification. PhymmBL proved useful in datasets in which no related sequences are present as it uses genomic features that may help identify distant taxa. The k-frequencies underperformed in all viral datasets.
PMCID: PMC3901335  PMID: 24438450
Viral metagenome; Assembler performance; Taxonomic classification; Chimera identification; Functional annotation
15.  BactPepDB: a database of predicted peptides from a exhaustive survey of complete prokaryote genomes 
With the recent progress in complete genome sequencing, mining the increasing amount of genomic information available should in theory provide the means to discover new classes of peptides. However, annotation pipelines often do not consider small reading frames likely to be expressed. BactPepDB, available online at, is a database that aims at providing an exhaustive re-annotation of all complete prokaryotic genomes—chromosomal and plasmid DNA—available in RefSeq for coding sequences ranging between 10 and 80 amino acids. The identified peptides are classified as (i) previously identified in RefSeq, (ii) entity-overlapping (intragenic) or intergenic, and (iii) potential pseudogenes—intergenic sequences corresponding to a portion of a previously annotated larger gene. Additional information is related to homologs within order, predicted signal sequence, transmembrane segments, disulfide bonds, secondary structure, and the existence of a related 3D structure in the Protein Databank. As a result, BactPepDB provides insights about candidate peptides, and provides information about their conservation, together with some of their expected biological/structural features. The BactPepDB interface allows to search for candidate peptides in the database, or to search for peptides similar to a query, according to the multiple properties predicted or related to genomic localization.
Database URL:
PMCID: PMC4221844  PMID: 25377257
16.  FunSecKB: the Fungal Secretome KnowledgeBase 
The Fungal Secretome KnowledgeBase (FunSecKB) provides a resource of secreted fungal proteins, i.e. secretomes, identified from all available fungal protein data in the NCBI RefSeq database. The secreted proteins were identified using a well evaluated computational protocol which includes SignalP, WolfPsort and Phobius for signal peptide or subcellular location prediction, TMHMM for identifying membrane proteins, and PS-Scan for identifying endoplasmic reticulum (ER) target proteins. The entries were mapped to the UniProt database and any annotations of subcellular locations that were either manually curated or computationally predicted were included in FunSecKB. Using a web-based user interface, the database is searchable, browsable and downloadable by using NCBI’s RefSeq accession or gi number, UniProt accession number, keyword or by species. A BLAST utility was integrated to allow users to query the database by sequence similarity. A user submission tool was implemented to support community annotation of subcellular locations of fungal proteins. With the complete fungal data from RefSeq and associated web-based tools, FunSecKB will be a valuable resource for exploring the potential applications of fungal secreted proteins.
Database URL:
PMCID: PMC3263735  PMID: 21300622
17.  Improving gene annotation of complete viral genomes 
Nucleic Acids Research  2003;31(23):7041-7055.
Gene annotation in viruses often relies upon similarity search methods. These methods possess high specificity but some genes may be missed, either those unique to a particular genome or those highly divergent from known homologs. To identify potentially missing viral genes we have analyzed all complete viral genomes currently available in GenBank with a specialized and augmented version of the gene finding program GeneMarkS. In particular, by implementing genome-specific self-training protocols we have better adjusted the GeneMarkS statistical models to sequences of viral genomes. Hundreds of new genes were identified, some in well studied viral genomes. For example, a new gene predicted in the genome of the Epstein–Barr virus was shown to encode a protein similar to α-herpesvirus minor tegument protein UL14 with heat shock functions. Convincing evidence of this similarity was obtained after only 12 PSI-BLAST iterations. In another example, several iterations of PSI-BLAST were required to demonstrate that a gene predicted in the genome of Alcelaphine herpesvirus 1 encodes a BALF1-like protein which is thought to be involved in apoptosis regulation and, potentially, carcinogenesis. New predictions were used to refine annotations of viral genomes in the RefSeq collection curated by the National Center for Biotechnology Information. Importantly, even in those cases where no sequence similarities were detected, GeneMarkS significantly reduced the number of primary targets for experimental characterization by identifying the most probable candidate genes. The new genome annotations were stored in VIOLIN, an interactive database which provides access to similarity search tools for up-to-date analysis of predicted viral proteins.
PMCID: PMC290248  PMID: 14627837
18.  Knowledge-Based Reconstruction of mRNA Transcripts with Short Sequencing Reads for Transcriptome Research 
PLoS ONE  2012;7(2):e31440.
While most transcriptome analyses in high-throughput clinical studies focus on gene level expression, the existence of alternative isoforms of gene transcripts is a major source of the diversity in the biological functionalities of the human genome. It is, therefore, essential to annotate isoforms of gene transcripts for genome-wide transcriptome studies. Recently developed mRNA sequencing technology presents an unprecedented opportunity to discover new forms of transcripts, and at the same time brings bioinformatic challenges due to its short read length and incomplete coverage for the transcripts. In this work, we proposed a computational approach to reconstruct new mRNA transcripts from short sequencing reads with reference information of known transcripts in existing databases. The prior knowledge helped to define exon boundaries and fill in the transcript regions not covered by sequencing data. This approach was demonstrated using a deep sequencing data set of human muscle tissue with transcript annotations in RefSeq as prior knowledge. We identified 2,973 junctions, 7,471 exons, and 7,571 transcripts not previously annotated in RefSeq. 73% of these new transcripts found supports from UCSC Known Genes, Ensembl or EST transcript annotations. In addition, the reconstructed transcripts were much longer than those from de novo approaches that assume no prior knowledge. These previously un-annotated transcripts can be integrated with known transcript annotations to improve both the design of microarrays and the follow-up analyses of isoform expression. The overall results demonstrated that incorporating transcript annotations from genomic databases significantly helps the reconstruction of novel transcripts from short sequencing reads for transcriptome research.
PMCID: PMC3270033  PMID: 22312447
19.  Phylogenomics of Prokaryotic Ribosomal Proteins 
PLoS ONE  2012;7(5):e36972.
Archaeal and bacterial ribosomes contain more than 50 proteins, including 34 that are universally conserved in the three domains of cellular life (bacteria, archaea, and eukaryotes). Despite the high sequence conservation, annotation of ribosomal (r-) protein genes is often difficult because of their short lengths and biased sequence composition. We developed an automated computational pipeline for identification of r-protein genes and applied it to 995 completely sequenced bacterial and 87 archaeal genomes available in the RefSeq database. The pipeline employs curated seed alignments of r-proteins to run position-specific scoring matrix (PSSM)-based BLAST searches against six-frame genome translations, mitigating possible gene annotation errors. As a result of this analysis, we performed a census of prokaryotic r-protein complements, enumerated missing and paralogous r-proteins, and analyzed the distributions of ribosomal protein genes among chromosomal partitions. Phyletic patterns of bacterial and archaeal r-protein genes were mapped to phylogenetic trees reconstructed from concatenated alignments of r-proteins to reveal the history of likely multiple independent gains and losses. These alignments, available for download, can be used as search profiles to improve genome annotation of r-proteins and for further comparative genomics studies.
PMCID: PMC3353972  PMID: 22615861
20.  AceView: a comprehensive cDNA-supported gene and transcripts annotation 
Genome Biology  2006;7(Suppl 1):S12.
Regions covering one percent of the genome, selected by ENCODE for extensive analysis, were annotated by the HAVANA/Gencode group with high quality transcripts, thus defining a benchmark. The ENCODE Genome Annotation Assessment Project (EGASP) competition aimed at reproducing Gencode and finding new genes. The organizers evaluated the protein predictions in depth. We present a complementary analysis of the mRNAs, including alternative transcript variants.
We evaluate 25 gene tracks from the University of California Santa Cruz (UCSC) genome browser. We either distinguish or collapse the alternative splice variants, and compare the genomic coordinates of exons, introns and nucleotides. Whole mRNA models, seen as chains of introns, are sorted to find the best matching pairs, and compared so that each mRNA is used only once. At the mRNA level, AceView is by far the closest to Gencode: the vast majority of transcripts of the two methods, including alternative variants, are identical. At the protein level, however, due to a lack of experimental data, our predictions differ: Gencode annotates proteins in only 41% of the mRNAs whereas AceView does so in virtually all. We describe the driving principles of AceView, and how, by performing hand-supervised automatic annotation, we solve the combinatorial splicing problem and summarize all of GenBank, dbEST and RefSeq into a genome-wide non-redundant but comprehensive cDNA-supported transcriptome. AceView accuracy is now validated by Gencode.
Relative to a consensus mRNA catalog constructed from all evidence-based annotations, Gencode and AceView have 81% and 84% sensitivity, and 74% and 73% specificity, respectively. This close agreement validates a richer view of the human transcriptome, with three to five times more transcripts than in UCSC Known Genes (sensitivity 28%), RefSeq (sensitivity 21%) or Ensembl (sensitivity 19%).
PMCID: PMC1810549  PMID: 16925834
21.  Identification of alternative splice variants in Aspergillus flavus through comparison of multiple tandem MS search algorithms 
BMC Genomics  2011;12:358.
Database searching is the most frequently used approach for automated peptide assignment and protein inference of tandem mass spectra. The results, however, depend on the sequences in target databases and on search algorithms. Recently by using an alternative splicing database, we identified more proteins than with the annotated proteins in Aspergillus flavus. In this study, we aimed at finding a greater number of eligible splice variants based on newly available transcript sequences and the latest genome annotation. The improved database was then used to compare four search algorithms: Mascot, OMSSA, X! Tandem, and InsPecT.
The updated alternative splicing database predicted 15833 putative protein variants, 61% more than the previous results. There was transcript evidence for 50% of the updated genes compared to the previous 35% coverage. Database searches were conducted using the same set of spectral data, search parameters, and protein database but with different algorithms. The false discovery rates of the peptide-spectrum matches were estimated < 2%. The numbers of the total identified proteins varied from 765 to 867 between algorithms. Whereas 42% (1651/3891) of peptide assignments were unanimous, the comparison showed that 51% (568/1114) of the RefSeq proteins and 15% (11/72) of the putative splice variants were inferred by all algorithms. 12 plausible isoforms were discovered by focusing on the consensus peptides which were detected by at least three different algorithms. The analysis found different conserved domains in two putative isoforms of UDP-galactose 4-epimerase.
We were able to detect dozens of new peptides using the improved alternative splicing database with the recently updated annotation of the A. flavus genome. Unlike the identifications of the peptides and the RefSeq proteins, large variations existed between the putative splice variants identified by different algorithms. 12 candidates of putative isoforms were reported based on the consensus peptide-spectrum matches. This suggests that applications of multiple search engines effectively reduced the possible false positive results and validated the protein identifications from tandem mass spectra using an alternative splicing database.
PMCID: PMC3146456  PMID: 21745387
22.  Identification of 3′ gene ends using transcriptional and genomic conservation across vertebrates 
BMC Genomics  2012;13:708.
In higher eukaryotes, gene expression is regulated at different levels. In particular, 3′UTRs play a central role in translation, stability and subcellular localization of transcripts. In recent years, the development of high throughput sequencing techniques has facilitated the acquisition of transcriptional data at a genome wide level. However, annotation of the 3′ ends of genes is still incomplete, thus limiting the interpretation of the data generated. For example, we have previously reported two different genes, ADD2 and CPEB3, with conserved 3′UTR alternative isoforms not annotated in the current versions of Ensembl and RefSeq human databases.
In order to evaluate the existence of other conserved 3′ ends not annotated in these databases we have now used comparative genomics and transcriptomics across several vertebrate species. In general, we have observed that 3′UTR conservation is lost after the end of the mature transcript. Using this change in conservation before and after the 3′ end of the mature transcripts we have shown that many conserved ends were still not annotated. In addition, we used orthologous transcripts to predict 3′UTR extensions and validated these predictions using total RNA sequencing data. Finally, we used this method to identify not annotated 3′ ends in rats and dogs. As a result, we report several hundred novel 3′UTR extensions in rats and a few thousand in dogs.
The methods presented here can efficiently facilitate the identification of not-yet-annotated conserved 3′UTR extensions. The application of these methods will increase the confidence of orthologous gene models across vertebrates.
PMCID: PMC3564943  PMID: 23244605
pre-mRNA cleavage site; PhyloP; RNA sequencing; TransMap
23.  In search of genome annotation consistency: solid gene clusters and how to use them 
3 Biotech  2013;4(3):331-335.
Maintaining consistency in genome annotations is important for supporting many computational tasks, particularly metabolic modeling. The SEED project has implemented a process that improves annotation consistencies across microbial genomes for proteins with conserved sequences and genomic context. In this research report, we describe this process and show how this effort has resulted in improvements to microbial genome annotations in the SEED. We also compare SEED annotation consistencies with other commonly used resources such as IMG (the Joint Genome Institute’s Integrated Microbial Genomes system), RefSeq (the National Center for Biotechnology Information’s Reference Sequence Database), Swiss-Prot (the annotated protein sequence database of the Swiss Institute of Bioinformatics, European Molecular Biology Laboratory and the European Bioinformatics Institute) and TrEMBL (Translated European Molecular Biology Laboratory nucleotide sequence data Library). Our analysis indicates that manual and computational efforts are paying off for the databases where consistency is a major goal.
PMCID: PMC4026451
Automatic annotation; Protein clusters
24.  MICheck: a web tool for fast checking of syntactic annotations of bacterial genomes 
Nucleic Acids Research  2005;33(Web Server issue):W471-W479.
The annotation of newly sequenced bacterial genomes begins with running several automatic analysis methods, with major emphasis on the identification of protein-coding genes. DNA sequences are heterogeneous in local nucleotide composition and this leads sometimes to sequences being annotated as authentic genes when they are not protein-coding genes or are true but uncharacterized protein-coding genes. This first annotation step is generally followed by an expert manual annotation of the predicted genes. The genomic data (sequence and annotations) organized in an appropriate databank file format is subsequently submitted to an entry point of the International Nucleotide Sequence Database. These procedures are inevitably subject to mistakes, and this can lead to unintentional syntactic annotation errors being stored in public databanks. Here, we present a new web program, MICheck (MIcrobial genome Checker), that enables rapid verification of sets of annotated genes and frameshifts in previously published bacterial genomes. The web interface allows one easily to investigate the MICheck results, i.e. inaccurate or missed gene annotations: a graphical representation is drawn, in which the genomic context of a unique coding DNA sequence annotation or a predicted frameshift is given, using information on the coding potential (curves) and annotation of the neighbouring genes. We illustrate some capabilities of the MICheck site through the analysis of 20 bacterial genomes, 9 of which were selected for their ‘Reviewed’ status in the National Center for Biotechnology Information (NCBI) Reference Sequence Project (RefSeq). In the context of the numerous re-annotation projects for microbial genomes, this tool can be seen as a preliminary step before the functional re-annotation step to check quickly for missing or wrongly annotated genes. The MICheck website is accessible at the following address: .
PMCID: PMC1160258  PMID: 15980515
25.  ProteinWorldDB: querying radical pairwise alignments among protein sets from complete genomes 
Bioinformatics  2010;26(5):705-707.
Motivation: Many analyses in modern biological research are based on comparisons between biological sequences, resulting in functional, evolutionary and structural inferences. When large numbers of sequences are compared, heuristics are often used resulting in a certain lack of accuracy. In order to improve and validate results of such comparisons, we have performed radical all-against-all comparisons of 4 million protein sequences belonging to the RefSeq database, using an implementation of the Smith–Waterman algorithm. This extremely intensive computational approach was made possible with the help of World Community Grid™, through the Genome Comparison Project. The resulting database, ProteinWorldDB, which contains coordinates of pairwise protein alignments and their respective scores, is now made available. Users can download, compare and analyze the results, filtered by genomes, protein functions or clusters. ProteinWorldDB is integrated with annotations derived from Swiss-Prot, Pfam, KEGG, NCBI Taxonomy database and gene ontology. The database is a unique and valuable asset, representing a major effort to create a reliable and consistent dataset of cross-comparisons of the whole protein content encoded in hundreds of completely sequenced genomes using a rigorous dynamic programming approach.
Availability: The database can be accessed through
PMCID: PMC2828119  PMID: 20089515

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