pairwise comparison local BLAST

Question

[michiel.karrenbelt]

Hi,

I have to perform multiple pairwise blast comparisons, via the command line interface, in order to check how well overlap sequence match (typically 1000 bases at one end should match 1000 bases at the start of the other). Can I do this without having to compile a database for each piece?

[Devon Ryan]

Is there a reason you want to use blast for this?

[michiel.karrenbelt]

I want to check the specificity of the overlaps

Answer 1

[Csaba Kerepesi]

Use the -subject option. But it will be faster if you generate database for each sequences.

Furthermore I recommend use as low word size (-word_size) as you can. Default word size of blastn (megablast) is 28 which may be too high for your purpose.

Answer 2

[Antonio R. Franco]

Or maybe you can define -task dc-megablast if you want to find sequences with not a very high homology