Blast a gene against one genome

Question

[olga.lubinsky]

Hello,

I want to run a blast of one gene against one genome. I have a fasta file of them both. Is there any way to run it other than converting the genome to a DB file?

Thank you in advance

[Nicolas Rosewick]

I don't think so. If you genome sequence is in NCBI's database you can blast a sequence against it.. unless a quick makeblastdb should make it.

edit Michael precises that -subject parameter should work in you case

Answer 1

[Michael]

makeblastdb takes a few seconds for a medium size genome. However, see the -subject parameter of blast+ binaries to accomplish this without a db.

It is advisable to create a blast database, because of

• low-complexity filtering and masking (recommended for whole genomes with repeats)
• being able to parse sequence ids (recommended when exported from genbank)
• easy retrieval of sequences by blastdbcmd
• entries can have additional annotation, e.g. individual taxon id (metagenomics)
• you'll always run blast twice

*** BLAST-2-Sequences options
 -subject <File_In>
   Subject sequence(s) to search
    * Incompatible with:  db, gilist, seqidlist, negative_gilist,
   db_soft_mask, db_hard_mask