Which vertebrate genomes are available for online BLAST, without the need to download them? There are only a few available through GenBank, more in Ensembl. However, many more vertebrate genomes are available through the NCBI ftb website. Do I have to download them first to be able to search by BLAST?
1 answer
Read this:
http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=FAQ#Batch
Basically you can use Web megablast and Network Blast to blast batch of sequences without downloading the databases. On the other hand , you can set up a local blast database and use standalone BLAST in your computer to do the blast. If you have fasta sequences for any organism it could be converted into blast database. Read the manual it has all the steps mentioned.
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