BLAST advanced options (Extension options)

Question

[cool_abbecker]

Can somebody please explain the "+++ Extension options" of blastn command line program? I am having difficulties to interpret when to use them based on the output of "blastn - help". The description is too short and uses a lot of vocabulary that I do not understand. I cannot find a BLAST manual that adequatly explains these options. A link where I can read an explanation would help a lot.

Answer 1

[Jean-Karim Heriche]

I suppose you're referring to the xdrop_ command line options, if not then please clarify.
Blast uses a heuristic in which a hit alignment is extended until the score drops below a threshold. This threshold is set as best score so far minus xdrop parameter value. This speeds up the alignment process at the cost of increasing the risk of getting a bad alignment.

[cool_abbecker]

So by setting the xdrop_command score to 999999 i force BLAST to do a full sequence alignment?

[GenoMax]

Based on your answer in the other question I think Blast is likely not the right tool for what you want to do (identify changes only in first part of sequence with the rest being almost invariant?). Are there sequences other than what you are interested in that need to be weeded out?

[cool.abbecker]

I want to identify species by nucleotide sequences. Instead of doing a BLAST followed by a global alignment of the top hits I want to do both in one step.