[BiO BB] Is there a good way to find orthologue sequences?

[Ryan Golhar]

Take a look at the following references.  They all put together ways of
finding orthologous sequences.  I'm using the database Ouyang
constructed.

Lee, Y., R. Sultana, et al. (2002). "Cross-Referencing Eukaryotic
Genomes: TIGR Orthologous Gene Alignments (TOGA)." Genome Res. 12(3):
493-502.

Mushegian, A. R., J. R. Garey, et al. (1998). "Large-Scale Taxonomic
Profiling of Eukaryotic Model Organisms: A Comparison of Orthologous
Proteins Encoded by the Human, Fly, Nematode, and Yeast Genomes." Genome
Res. 8(6): 590-598.

Ouyang, M., J. Case, et al. (2003). "Five Hundred Sixty-Five Triples of
Chicken, Human, and Mouse Candidate Orthologs." Journal of Molcular
Evolution 57(3): 271-281.



-----
Ryan Golhar
Computational Biologist
The Informatics Institute at
The University of Medicine & Dentistry of NJ

Phone: 973-972-5034
Fax: 973-972-7412
Email: golharam at umdnj.edu

-----Original Message-----
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[mailto:bio_bulletin_board-bounces+ryangolhar=hotmail.com at bioinformatics
.org] On Behalf Of yezhiqiang at gmail.com
Sent: Friday, June 17, 2005 1:49 PM
To: bio_bulletin_board at bioinformatics.org
Subject: [BiO BB] Is there a good way to find orthologue sequences?


Dear all,
    Is there a good way to find orthologue sequences? I mean, I have a
protein sequence in species A, how could I get all the available
corresponding sequences from other species?  I blast my sequence to nr,
there are just too many hits with low e-value and high identity, so that
some "corresponding" sequences from distant related species could not be
find by blast. Is there any good method for automatically solve this
problem?

    Thank you very much. _______________________________________________
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