HOW TO COMPARE TWO BLAST OUPUTS

Question

[iamtuttu5]

I want to compare two blastx results , which is generated blastx.outfmt6 format , How to perform this task ?

example for first file is

assembly_c1 At2g07698_2 92.25 271 19 1 27 833 78 348 1.00E-178 508

assembly_c2 At1g07540 30.77 52 36 0 72 227 504 555 0.62 30.8

assembly_c3 AtCh073 80.43 46 9 0 29 166 69 114 7.00E-19 81.3

assembly_c4 At1g61520 68.85 61 16 1 53 235 18 75 4.00E-21 86.7

assembly_c6 AtCh024 88 50 6 0 303 452 77 126 2.00E-23 93.6

assembly_c7 At2g05100 83.71 178 29 0 67 600 1 178 2.00E-109 319

assembly_c8 At2g39730 92.93 184 13 0 25 576 138 321 2.00E-125 367

example for second file is

At1g23940_3 KOG1062 1.00E-128 51 454 1 349 11 397 866 Vesicle coat complex AP-1, gamma subunit U Intracellular trafficking, secretion, and vesicular transport

At1g49670_1 KOG4169 6.00E-82 51 298 1 287 1 261 261 15-hydroxyprostaglandin dehydrogenase and related dehydrogenases IR Multiple classes

At2g34520_2 KOG1741 3.00E-20 60 90.8 1 70 34 103 103 Mitochondrial/chloroplast ribosomal protein S14/S29 J Translation, ribosomal structure and biogenesis

At4g02660_1 KOG1788 0 89 4889 1 2806 1 2799 2799 Uncharacterized conserved protein S Function unknown

At4g17620_1 KOG3116 8.00E-05 22 44.1 660 779 55 172 177 Predicted C3H1-type Zn-finger protein R General function prediction only

At5g28230_2 KOG0987 4.00E-14 40 70.1 7 99 231 347 540 DNA helicase PIF1/RRM3 D Cell cycle control, cell division, chromosome partitioning

CE00494_2 KOG1192 4.00E-42 32 166 145 398 229 491 496 UDP-glucuronosyl and UDP-glucosyl transferase GC Multiple classes

CE16400_2 KOG0817 1.00E-31 34 130 1 140 5 142 142 Acyl-CoA-binding protein I Lipid transport and metabolism

CE16400_2 KOG4177 4.00E-07 41 49.6 165 238 542 609 1143 Ankyrin M Cell wall/membrane/envelope biogenesis

CE18903_1 KOG3645 5.00E-64 19 239 1 444 1 449 449 Acetylcholine receptor T Signal transduction mechanism

Is there any tool or script to perform this

Any help will be appreciated

Thank you

[Pierre Lindenbaum]

what do you want to compare ?

[iamtuttu5]

I got two results from Blast as two output file in outfmt6 format I want to find out At2g07698_2 in the second file if present and the details related to it like KOG ID and the function

[Joe]

cat blastfile1 | grep "At2g07698_2" && cat blastfile2 | grep "At2g07698_2"

Would be a nice quick way to get all the lines in both file that have your hit if that is what you want, it's not clear to me. && means that the second command will only execute of the first is successful, i.e. your search term is found.

Then cut and sort are your friends as Pierre said.

Answer 1

[Pierre Lindenbaum]

this is a basic linux task; Search google for sort+join . sort http://man7.org/linux/man-pages/man1/sort.1.html and join http://man7.org/linux/man-pages/man1/join.1.html

[iamtuttu5]

Thank you so much pierre :-)