Comparing BLAST m8 Outputs

[JollofScientist]

Hi,

I want to compare BLAST outputs in m8 format to find out if any queries in the separate output files have the same subject hits to NCBI nr database.

For example, for the 2 BLAST outputs in m8 format below, displaying only the query and subject columns, I want to find PFD1 and GHT3 have the same hit (Hsp90):

BLAST Output 1:

PFD1 Hsp90
PFD2 Gan80
PFD5 Kan38

BLAST Output 2:

GHT1 Lsg70
GHT2 Jkl78
GHT3 Hsp90
GHT6 Odf45


Any help, suggestions or recommendations will be greatly appreciated. Also let me know if you have any questions.

[TiborNagy]

You can write a custom script, where a hash key is the second column (preferred), or you can write some shell script like this:
awk '{print $2}' blast1 | sort >a; awk '{print $2}' blast2 | sort >b; comm -12 a b >common.txt; for i in `cat common.txt`; do grep $i blast1 blast2; done

But you can combine the querys to one file and run Blast with that.

[lindenb]

cross posted on biostars: http://www.biostars.org/p/90325/

[JollofScientist]

Thanks for the help. Rookie mistake with the cross post. It won't happen again.