[ssml] Small Genome Similarity

[Mensur Dlakic]

This genome is small enough that it might be worth using Ewan Birney's WISE 
tools (http://www.ebi.ac.uk/Wise2/ and 
ftp://ftp.ebi.ac.uk/pub/software/unix/wise2/) to look for matches against 
PFAM or any PFAM-like database of HMMs. Ordinarily, this method is 
dreadfully slow (it's that old theme of sensitivity vs. speed), but 2.4kb 
should be manageable. This will take care of possible frameshifts because 
the program knows how to deal with them. Aside from this, I would work only 
with predicted ORFs, as viral genomes are known to be very divergent and it 
doesn't surprise me that you don't see much similarity at DNA level. Last 
time I tried it, Glimmer did OK on viral genomes, especially if you filter 
the initial results with RBSFinder (both programs are available at 
http://www.tigr.org/software/).

Cheers,

Mensur

At 05:06 PM 2/12/2004, you wrote:
>i All,
>
>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

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