BLAST Output of the Alignment
I have BLAST results that I want to export the output to show the alignment. To explain, I have a 500nt sequence I have aligned with multiple other sequences. I want that output to show where these alignments lie in retrospect to this 500nt sequence, for example:
AAACTCTGCGATCTTTTCCC....AAACTCTGCGATCTTTTCCC(up to 500nt) AACTGCT
AAACTCTGCGATCTTTTCCC....AAACTCTGCGATCTTTTCCC(up to 500nt) CTTTTCCCC
Anybody know how to achieve this?
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Little confused: do you have a blast output of hits you want to multiple align? do you already have a multiple alignment and want to add a new sequences to it? can you elaborate a bit?
I think I know what you mean... If you open the file with your BLAST results do you see somewhere the alignments that you want? If yes you could use something like biopython.
you find code for biopython here http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc102
If he only wants to get the alignment part out of the blast result , you're better of asking for the extended m8 out format and simply select the column with the alignment