hi, dear guys
I performance blastn (-m 8) using a query file of many sequences, and for each query sequence, the output contains many fragmental hits of significance.
however, these hits have no overlap, and what is interesting is that most gaps < 300bp (much shorter than full-length of the query sequence).
so, how can i concatenate those closely related hits into one via setting a value (e.g 300bp) when these hits match the same subject (different regions), ——also to reduce the number of output hits per query.
for example:
http://www.freeimagehosting.net/bohcp
are there any scripts or tools for this purpose?
all your replies are welcome!