[Genome] finding homologe gene

[Kayla Smith]

Hello Keren,

Please see this previously answered mailing list question about how to 
use our tools to find sequence matches to the genome:

http://www.soe.ucsc.edu/pipermail/genome/2006-March/009918.html

I hope this is helpful to you.  Please don't hesitate to contact us 
again if you require further assistance.

Kayla Smith
UCSC Genome Bioinformatics Group



statement.

Keren Avital wrote:
> Hello, 
> 
> Im trying to find a homologe gene to a pseudogene by using Blat.
> But im getting too many results, some of them have very short matches comparing to the sequence length.
> How can I tell if a result is good enough to be a homologe gene?
> 
> For example, im trying to find: 
> 
> ATGGAAATGATGTCAG
> CAAAAAGAAAATTCAAGCGATTTTCTTATTCAAGTTCAAAATGGGTCGTAAAGCAGCAGAGACAACTTGC
> AACATCGACTGCGCATCTGGTCCAGGAACTGCTAACGAACGTACAGTGCAGTCGTGGTTCAAAAAGTTTT
> GCAAAGGAGAGGAGAACCTCGAAGATGAGGAATGTAGTGGCCGGCCGTTGGAAGTTGACAACCACCAATT
> GAGAGCAATCATTGAAGCTGATCCTCTTACAACTATACAAGAAGTTGCTGAAGAACTCAACCTTGACCAT
> TCTATGGTCGTTTGGCATTTGAAGCAAATTGGAAAGATGAAAAAGCTCGATAAGTGGGTGCCTCATGAGC
> TGAGCAAAAATCAAATCATCATTTTGAAGTGTCGTCATCTCTTATTCTACGCAACAATGAACCATTTCTC
> AATTGGATTGGGACATGGCAATGAAAAGTGTATTGTATGTGACAACCTGCTACAAGCAGCTCAGTGGTTG
> GACCAGGAAGCTGCAAAGCACTTCTCAAAGCCAAATTTGCACCAAAAAAAAAGGTCATGGTCACTGTTTG
> GCACTGTGATCCACTACAGCTTTCTGAATCCCAGCGAAACCATTACCTCTGATAAGCATGCTCAGAAAAT
> GAGATGGAAATGAGATGCACCGAAAACTGCAATGCCTGCAGCCGGCACTGGTCAACAGAAAGGGCCCAGT
> TCTTTACGACAAGGCCTGACCTCATGTTGCACAACCGACACTTCAAAAGTTGAATGAATTGGGCTACGAA
> GTTTTGCCTCATCTGCCATATTCACCTGACCTCTCGCCGATCGACTACCACTTCTTCCAACTTTTTGCAG
> GGAAAATGTTTCCACAATCAGCAGGATGCCGAAAATGCTTCCAAGGGTTTGTTGAATCCCAAAGCACAGA
> TTTTTACACTACAGGAATAAACAAATTTATTCCTCATTGGCAAAAATGTGTTGATTGTAATGGTTCCTAA
> TTTGAGTAA
> 
> And Im getting too  much results, some of them have very few matches.
> 
> If you have another way to find homologe genes for pseudogene that would help too...
> 
> Thanks,
> Keren
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome