BLAST fasta format to other fasta

Question

[loly.pearl86]

Hi,

Can someone help me how can i BLAST my fasta sequences candidate to other specific species which is in fasta format (Trinity.fasta sequences) Both of them on my computer (the fast for the other species and my candidate fasta.sequences)

I know how to used BLAST in NCBI but it take long time as the fasta file is too large .So i want to know other method please

Thanks

Answer 1

[GenoMax]

You can use local blast. There are versions of blast+ available for most operating systems (including windows). You can download the latest blast+ executables here: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/.

If you are not familiar with the command line it may be a bit of a learning curve but you can take a look at the blast+ tutorial here.

Answer 2

[h.mon]

AS genomax2 said, you could do this easily with local BLAST. However, BLAST may be too slow, so you could also try DIAMOND - the limitation is your database has to be protein, but the query may be either nucleotides or proteins.