Question: Bl2Seq With Multi Fasta
3
gravatar for Jacek
8.8 years ago by
Jacek100
USA
Jacek100 wrote:

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

fasta blast • 3.1k views
ADD COMMENTlink modified 8.7 years ago by Darked894.2k • written 8.8 years ago by Jacek100

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

ADD REPLYlink written 8.8 years ago by Michael Schubert6.9k
5
gravatar for Neilfws
8.8 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

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
ADD COMMENTlink modified 8.8 years ago • written 8.8 years ago by Neilfws48k
  1. Use a dedicated alignment tool instead of blast.
ADD REPLYlink written 8.8 years ago by Michael Schubert6.9k
0
gravatar for Darked89
8.8 years ago by
Darked894.2k
Barcelona, Spain
Darked894.2k wrote:

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.

ADD COMMENTlink written 8.8 years ago by Darked894.2k
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