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Old 09-07-2012, 09:38 PM   #1
Tsuyoshi
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Location: japan

Join Date: Sep 2012
Posts: 24
Question how to output only one best-hit result using standalone blast

Hello
I am running standalone blast now to blastp a protein data set against a genome data.

Although I have set the best-hits filtering algorithm, namely, using -best_hit_overhang, and the value I set was 0.25 (0.1~0/25 was recommended at http://www.ncbi.nlm.nih.gov/books/NB...stHits_filteri)

Compared the results without -best_hit_overhang, indeed, the number of matches for each inquery was eliminated a lot, however, what I want is to output just one best hit result (according to the bit score and evalue).

For example, the output result was like
***************************************************************
gi|270118727|emb|CAT18807.1| gi|323452346|gb|EGB08220.1| 26.15 65 48 0 31 95 835 899 0.05 35.4
gi|270118727|emb|CAT18807.1| gi|323451569|gb|EGB07446.1| 28.77 73 46 2 226 298 14 80 0.42 31.2
gi|270118727|emb|CAT18807.1| gi|323445796|gb|EGB02232.1| 30.65 62 43 0 349 410 111 172 1.8 29.3
gi|270118727|emb|CAT18807.1| gi|323449782|gb|EGB05667.1| 29.27 41 29 0 132 172 105 145 2.1 29.6
gi|270118727|emb|CAT18807.1| gi|323448614|gb|EGB04510.1| 26.92 52 38 0 189 240 15 66 6.5 27.7
***************************************************************

And I just want the top best one,
***************************************************************
gi|270118727|emb|CAT18807.1| gi|323452346|gb|EGB08220.1| 26.15 65 48 0 31 95 835 899 0.05 35.4
***************************************************************

Would anyone please help to tell me how to do that?
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