I've been sequencing, assembling, and annotating quite a few liver and spleen transcriptomes from wild rodents, and I have noticed that many of the assembled transcripts don't get blast hits to other rodents or mammals. Through some broader blasting, I've discovered that some of the transcripts may be viral. Can anyone recommend a good database (that I can download) to blast against to try to specifically identify viral transcripts? I'm hoping for a database that excludes everything except potential pathogens.
As far as I know NCBI has discontinued their non redundant database (it included all species). They do have a quite elaborate nr version for sequence cleaning (UniVec). That as well wouldn't suit your purpose as it focuses on plasmids and adapter sequences.
EBI has something similar but much less redundant which again is not based on viruses but rather on plasmids etc..
I fear that what you have to do is select all viral sequences from your favorite database and make them non redundant yourself.
Uniprot has databases that are taxon-specific. Here's a link for their virus database: http://www.uniprot.org/uniprot/?query=taxonomy%3a10239&format=*
try the refseq viral division at ncbi:
https://www.ncbi.nlm.nih.gov/genomes/GenomesHome.cgi?taxid=10239
fasta are available for download here:
ftp://ftp.ncbi.nih.gov/refseq/release/viral/
1. You can try BLASTing your sequences against one of the following databases:
http://www.viprbrc.org/brc/home.spg?decorator=vipr
http://www.biovirus.org/
2. I still think that you can enhance the sensitivity of your BLAST search at NCBI by:
• Select tBLASTx program that searches translated nucleotide database using a translated nucleotide query.
• Try different nucleotide databases (e.g nr/nt, refseq-genomic, est, gss..).
• Use the organism selection function to include viruses only or you can even widen your search by using the “Exclude” option and to do the search excluding mammals or eukaryotes.
Thanks everyone for the responses. I'm going to give Uniprot a shot.
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