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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!
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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. -
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.Originally posted by sphil View Post
Thanks a lot for your wise words Phil! appreciate you taking time out to reply
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no worries...!Comment
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