[BiO BB] Is there a good way to find orthologue sequences?
golharam at umdnj.edu
Mon Jun 20 00:13:38 EDT 2005
Take a look at the following references. They all put together ways of
finding orthologous sequences. I'm using the database Ouyang
Lee, Y., R. Sultana, et al. (2002). "Cross-Referencing Eukaryotic
Genomes: TIGR Orthologous Gene Alignments (TOGA)." Genome Res. 12(3):
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.
The Informatics Institute at
The University of Medicine & Dentistry of NJ
Email: golharam at umdnj.edu
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.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?
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
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