Bl2Seq With Multi Fasta

Question

[Jacek]

Hello,

I have two groups of sequences in separate files (1.fasta and 2.fasta). I need to make comparison between them. However I cannot run

bl2seq -i 1.fa -j 2.fa -p blastp -o output

because bl2seq is expecting only one sequence in a fasta file.

Is splitting multi fasta files the only option to compare each sequence in 1.fa with each sequence in 2.fa?

Thanks for help

[Michael Schubert]

Is there any reason you don't use a dedicated alignment tool instead of blast?

Answer 1

[Neilfws]

Correct: bl2seq, as the name suggests - "BLAST 2 sequences" - is for the comparison of one sequence to another.

You have 3 options:

1. Split the multi-fasta files into separate sequences; lots of tools to do this, some have been discussed at this site
2. Use formatdb to create a BLAST database from one of the multi-fasta files and BLAST the other against it
3. See Michael's comment, below

[Michael Schubert]

1. Use a dedicated alignment tool instead of blast.

Answer 2

[Darked89]

For a small number of short sequences (say 20 ESTs vs 4 splice forms) you may use dotplot (program: dotter). It is easy to see rearrangements or regions of high/low similarity. Not good if you need hard numbers.