Question: HOW TO COMPARE TWO BLAST OUPUTS
1
gravatar for iamtuttu5
4.0 years ago by
iamtuttu540
United States
iamtuttu540 wrote:

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

ADD COMMENTlink modified 3.4 years ago by Biostar ♦♦ 20 • written 4.0 years ago by iamtuttu540
2

what do you want to compare ?

ADD REPLYlink written 4.0 years ago by Pierre Lindenbaum129k
1

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

ADD REPLYlink written 4.0 years ago by iamtuttu540

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.

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by Joe17k
1
gravatar for Pierre Lindenbaum
4.0 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum129k wrote:

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

ADD COMMENTlink written 4.0 years ago by Pierre Lindenbaum129k
1

Thank you so much pierre :-)

ADD REPLYlink written 4.0 years ago by iamtuttu540
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