Literature DB >> 24980400

Overview and comparison of ortholog databases.

Andrey Alexeyenko1, Julia Lindberg1, Asa Pérez-Bercoff1, Erik L L Sonnhammer2.   

Abstract

Orthologs are an indispensable bridge to transfer biological knowledge between species, from protein annotations to sophisticated disease models. However, orthology assignment is not trivial. A large number of resources now exist, each with its own idiosyncrasies. The goal of this review is to compare their contents and clarify which database is most suited for a certain task.: � 2006 Elsevier Ltd . All rights reserved.

Year:  2006        PMID： 24980400     DOI： 10.1016/j.ddtec.2006.06.002

Source DB:  PubMed          Journal:  Drug Discov Today Technol        ISSN： 1740-6749


  15 in total

1.  OrthoInspector: comprehensive orthology analysis and visual exploration.

Authors:  Benjamin Linard; Julie D Thompson; Olivier Poch; Odile Lecompte
Journal:  BMC Bioinformatics       Date:  2011-01-10       Impact factor: 3.169

2.  Characterization of the genome and serine protease of a novel Bacillus subtilis isolate.

Authors:  Zahoor Khan; Maryam Shafique; Faizan Saleem; M Kamran Azim; Nusrat Jabeen; Sehar Afshan Naz
Journal:  Antonie Van Leeuwenhoek       Date:  2022-01-15       Impact factor: 2.271

3.  Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees.

Authors:  Brigitte Boeckmann; Marc Robinson-Rechavi; Ioannis Xenarios; Christophe Dessimoz
Journal:  Brief Bioinform       Date:  2011-07-07       Impact factor: 11.622

4.  Domain architecture conservation in orthologs.

Authors:  Kristoffer Forslund; Isabella Pekkari; Erik L L Sonnhammer
Journal:  BMC Bioinformatics       Date:  2011-08-05       Impact factor: 3.169

5.  Toward community standards in the quest for orthologs.

Authors:  Christophe Dessimoz; Toni Gabaldón; David S Roos; Erik L L Sonnhammer; Javier Herrero
Journal:  Bioinformatics       Date:  2012-02-12       Impact factor: 6.937

6.  The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.

Authors: 
Journal:  PLoS Comput Biol       Date:  2009-07-03       Impact factor: 4.475

7.  Joining forces in the quest for orthologs.

Authors:  Toni Gabaldón; Christophe Dessimoz; Julie Huxley-Jones; Albert J Vilella; Erik Ll Sonnhammer; Suzanna Lewis
Journal:  Genome Biol       Date:  2009-09-29       Impact factor: 13.583

8.  MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement.

Authors:  Guanqun Shi; Liqing Zhang; Tao Jiang
Journal:  BMC Bioinformatics       Date:  2010-01-06       Impact factor: 3.169

9.  InParanoid 7: new algorithms and tools for eukaryotic orthology analysis.

Authors:  Gabriel Ostlund; Thomas Schmitt; Kristoffer Forslund; Tina Köstler; David N Messina; Sanjit Roopra; Oliver Frings; Erik L L Sonnhammer
Journal:  Nucleic Acids Res       Date:  2009-11-05       Impact factor: 16.971

10.  ANCAC: amino acid, nucleotide, and codon analysis of COGs--a tool for sequence bias analysis in microbial orthologs.

Authors:  Arno Meiler; Claudia Klinger; Michael Kaufmann
Journal:  BMC Bioinformatics       Date:  2012-09-08       Impact factor: 3.169
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