[BiO BB] [Fwd: Small Genome Similarity]

[Martin Gollery]

Tristan,

   Try going to Blosum30 for the matrix, and lower the open and extend gap 
penalties, and lower the reporting threshold. Use the mito codons. If you still 
don't get hits, switch from BLAST to Smith-Waterman, or use Interproscan to 
compare it to several signature databases.

Marty

Quoting "J.W. Bizzaro" <jeff at bioinformatics.org>:

>I am looking at a novel 2.4 KB viral genome and want to see if anything 
>homologous is known. 
>
>Have tried blastn,blastx variants but nothing comes up (possibly due to 
>frame or simply divergence). 
>
>This beastie may replicate in the mitochondria of vertebrates so 
>translations may need to use mito not nuclear codons. 
>
>Please let me know if you have any suggestions or experience looking at 
>similar sequences. 
>
>Thank you, 
>
>Tristan 




Martin Gollery
Associate Director
Center For Bioinformatics
University of Nevada at Reno
Dept. of Biochemistry / MS330
775-784-7042


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