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1.  A meta-approach for improving the prediction and the functional annotation of ortholog groups 
BMC Genomics  2014;15(Suppl 6):S16.
In comparative genomics, orthologs are used to transfer annotation from genes already characterized to newly sequenced genomes. Many methods have been developed for finding orthologs in sets of genomes. However, the application of different methods on the same proteome set can lead to distinct orthology predictions.
We developed a method based on a meta-approach that is able to combine the results of several methods for orthologous group prediction. The purpose of this method is to produce better quality results by using the overlapping results obtained from several individual orthologous gene prediction procedures. Our method proceeds in two steps. The first aims to construct seeds for groups of orthologous genes; these seeds correspond to the exact overlaps between the results of all or several methods. In the second step, these seed groups are expanded by using HMM profiles.
We evaluated our method on two standard reference benchmarks, OrthoBench and Orthology Benchmark Service. Our method presents a higher level of accurately predicted groups than the individual input methods of orthologous group prediction. Moreover, our method increases the number of annotated orthologous pairs without decreasing the annotation quality compared to twelve state-of-the-art methods.
The meta-approach based method appears to be a reliable procedure for predicting orthologous groups. Since a large number of methods for predicting groups of orthologous genes exist, it is quite conceivable to apply this meta-approach to several combinations of different methods.
PMCID: PMC4240552  PMID: 25573073
ortholog; homolog; meta-approach; sequences-profile comparison
2.  BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms 
Advances in Bioinformatics  2012;2012:893048.
The pairwise comparison of RNA secondary structures is a fundamental problem, with direct application in mining databases for annotating putative noncoding RNA candidates in newly sequenced genomes. An increasing number of software tools are available for comparing RNA secondary structures, based on different models (such as ordered trees or forests, arc annotated sequences, and multilevel trees) and computational principles (edit distance, alignment). We describe here the website BRASERO that offers tools for evaluating such software tools on real and synthetic datasets.
PMCID: PMC3366197  PMID: 22675348
3.  Counting RNA Pseudoknotted Structures 
Journal of Computational Biology  2011;18(10):1339-1351.
In 2004, Condon and coauthors gave a hierarchical classification of exact RNA structure prediction algorithms according to the generality of structure classes that they handle. We complete this classification by adding two recent prediction algorithms. More importantly, we precisely quantify the hierarchy by giving closed or asymptotic formulas for the theoretical number of structures of given size n in all the classes but one. This allows us to assess the tradeoff between the expressiveness and the computational complexity of RNA structure prediction algorithms.
PMCID: PMC3179619  PMID: 21548808
algorithms; combinatorics; computational molecular biology; probability; strings
4.  VARNA: Interactive drawing and editing of the RNA secondary structure 
Bioinformatics  2009;25(15):1974-1975.
Description: VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases.
Features: VARNA implements four drawing algorithms, supports input/output using the classic formats dbn, ct, bpseq and RNAML and exports the drawing as five picture formats, either pixel-based (JPEG, PNG) or vector-based (SVG, EPS and XFIG). It also allows manual modification and structural annotation of the resulting drawing using either an interactive point and click approach, within a web server or through command-line arguments.
Availability: VARNA is a free software, released under the terms of the GPLv3.0 license and available at
Supplementary information: Supplementary data are available at Bioinformatics online.
PMCID: PMC2712331  PMID: 19398448

Results 1-4 (4)