Score bit in multiple BLAST

Question

[m.shahdoost]

Hi I want to blast two data-sets with each other. actually I want the bit score of pairwise blast of two data-sets. But I have a little information about its possibility and also the appropriate software for this job. Please help me.

[GenoMax]

You can blast the two groups against each other using the command line blast. Here is the manual to get you started.

If the sequences are homologous (and are longer than 25-30 characters) then blat could also be used.

Answer 1

[Chirag Nepal]

You can use BLAST (blastall -p blastn -i INPUTFASTA -d YOURDATASET -e EVALUECUTOFF -m 8) to get bit-score or e-value between two or more sequences. Using -m 8, gives the output in tabular matrix making it easier to parse. For more parameters, refer to the blast help options.