Best hit alignment in offline Blast

[ron128]

Hello. Can anyone let me know the proper command and syntax for best hit alignment in offline blast? The blast manual lists is not very clear on this topic, and I cannot seem to find much information about this elsewhere on the net. Should i use only -best_hit_overhang & -best_hit_score_edge as the two options for getting a best hit alignment? Also, what would be an optimal parameters for -best_hit_score_edge? My dataset contains lots of smaller sequences (roughly about 100 bases in length), so I would want them to be ideally covered in my blast sequences. Thanks a ton!

[sphil]

Usually BLAST reports the found HSP ordered. Which means that the first hit reported also is the best hit with respect to E-value / Bit Score... so you just want to parse the first hit from every input-sequence. You have to keep in mind that if there are hits that are equally good you end up with kind of ambigous results because they are still listed.

[ron128]

You have to keep in mind that if there are hits that are equally good you end up with kind of ambigous results because they are still listed.

This is what I am afraid of if I blast my sequences to the NR or NT database. To circumvent this, since I am dealing with human data, I am blasting only against Human est sequences. I am hoping this will take care of the problem.

Thanks a lot for your wise words Phil! appreciate you taking time out to reply

[sphil]

no worries...!