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Nucleic Acids Research Advance Access originally published online on May 5, 2007
Nucleic Acids Research 2007 35(Web Server issue):W678-W682; doi:10.1093/nar/gkm278
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Nucleic Acids Research, 2007, Vol. 35, No. suppl_2 W678-W682
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

BLASTO: a tool for searching orthologous groups

Yi Zhou and Laura F. Landweber*

Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA

*To whom correspondence should be addressed: Tel: +1 609 258 1947; Fax: +1 609 258 7892; Email: lfl{at}princeton.edu

Received January 31, 2007. Revised April 6, 2007. Accepted April 11, 2007.

We present BLAST on Orthologous groups (BLASTO), a modified BLAST tool for searching orthologous group data. It treats each orthologous group as a unit and outputs a ranked list of orthologous groups instead of single sequences. By filtering out redundancy and putative paralogs, sequence comparisons to orthologous groups, instead of to single sequences in the database, can improve both functional prediction and phylogenetic inference. BLASTO computes the significance score of each orthologous group based on the individual BLAST hits in the orthologous group, using the number of taxa in the group as an optional weight. This allows users to control the species diversity of the orthologous groups. BLASTO incorporates the best-known multispecies ortholog databases, including NCBI Clusters of Orthologous Group, NCBI euKaryotic Orthologous Group database, OrthoMCL, MultiParanoid and TIGR Eukaryotic Gene Orthologues database, and offers a useful platform to integrate orthology information into functional inference and evolutionary studies of individual sequences. BLASTO is accessible online at http://oxytricha.princeton.edu/BlastO.


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F. Schreiber, G. Worheide, and B. Morgenstern
OrthoSelect: a web server for selecting orthologous gene alignments from EST sequences
Nucleic Acids Res., July 1, 2009; 37(suppl_2): W185 - W188.
[Abstract] [Full Text] [PDF]


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