remove duplicated entries from BLAST result file

Question

[Kumar]

How I can remove duplicated entries from command line BLAST results file.

Thanks,

[Pierre Lindenbaum]

define "duplicatedentries". Hsp ? Hit ?

[Kumar]

thanks,

Could you describe this in command format.

[Ram]

Sure.

echo "What do you mean by \"duplicated entries\"? Are you referring to HSPs, hits, or something else entirely?"

[Kumar]

Yes, i mean duplicate hits. as an example, like >gi|10001|, >gi|1000| such as duplicate entries..

[Ram]

Are these duplicate hits seen for the same query? If they are seen for different queries, they are not duplicates - just asking so we are closer to defining the problem.

[Kumar]

Yes..these are the duplicate hits that generated by same hits..is any way at command line BLAST to remove these type of all duplicated hits from result file.

[Ram]

I'm sorry, duplicate hits by same hits? Are you referring to multiple HSPs perhaps? Remember, each query can have multiple hits. Each hit can have multiple HSPs. Can you give us a sample maybe?

I don't think BLAST would give you a multiple hits where the subject as well as the query are the same sequence. BLAST would just specify them as a single hit with multiple HSPs, unless we are dealing with repeat sequences, in which case repeatmasker could be a prudent pre-processing step.

[jrparedesmontero]

Hey RamRS.

I have an HSPs table. There are some cases in which queries of different length hit regions of the subject that overlap. The table has a column with the coordinates per HPS. I am interested in removing the redundant HPSs, is there a script available I can use. Thanks in advance for your reply.