Question: Visualization of tblastn results
0
gravatar for arronar
5.6 years ago by
arronar200
Austria
arronar200 wrote:

Hello.

i am creating a web interface application , that in one step , it runs localy tblastn (a contig against sra database). So the output of the tblastn is something like this :

 

Sequences producing significant alignments:                          (Bits)  Value

  gnl|SRA|SRR035297.39.2 FHVGOOJ04CK0DZ.2 length=269                    181   9e-52
  gnl|SRA|SRR035296.111121.2 FIQ4L3X01ALQH7.2 length=272                169   2e-47
  gnl|SRA|SRR035294.69335.2 FIHSSUW01CW10W.2 length=269                 167   8e-47
  gnl|SRA|SRR035296.21075.2 FIQ4L3X01BYI0R.2 length=243                 162   2e-45
  .......
  .......
> gnl|SRA|SRR035297.39.2 FHVGOOJ04CK0DZ.2 length=269
Length=269

 Score =   181 bits (458),  Expect = 9e-52, Method: Composition-based stats.
 Identities = 84/89 (94%), Positives = 88/89 (99%), Gaps = 0/89 (0%)
 Frame = -2

Query  855  QGAGEDRLVLLKGVSGAFRPGVLTALMGVSGAGKTTLMDVLAGRKTGGYIDGEIKISGYP  914
            QG G+DRL+LLKGVSGAFRPGVLTALMGVSGAGKTTLMDVLAGRKTGGYIDGEIKISGYP
Sbjct  268  QGMGDDRLLLLKGVSGAFRPGVLTALMGVSGAGKTTLMDVLAGRKTGGYIDGEIKISGYP  89

Query  915  KKQETFARISGYCEQNDIHSPYVTVYESL  943
            KKQETF+RISGYCEQNDIHSPYVT+YESL
Sbjct  88   KKQETFSRISGYCEQNDIHSPYVTLYESL  2


> gnl|SRA|SRR035296.111121.2 FIQ4L3X01ALQH7.2 length=272
Length=272

 Score =   169 bits (427),  Expect = 2e-47, Method: Compositional matrix adjust.
 Identities = 78/90 (87%), Positives = 84/90 (93%), Gaps = 0/90 (0%)
 Frame = +2

Query  896  AGRKTGGYIDGEIKISGYPKKQETFARISGYCEQNDIHSPYVTVYESLVYSAWLRLPQDV  955
            AGRKTGGYIDGEIKISGYPKKQETF+RISGYCEQNDIHSPYVT+YESL+YSAWLRLP DV
Sbjct  2    AGRKTGGYIDGEIKISGYPKKQETFSRISGYCEQNDIHSPYVTLYESLLYSAWLRLPSDV  181

Query  956  DEKTRKMFVDEVMELVELGPLRSALVGLPG  985
            +E  RK+FV+EVM LVEL PLR ALVGLPG
Sbjct  182  NETQRKLFVEEVMNLVELSPLRDALVGLPG  271
.......
.......

So i want to ask if its possible to visualize those results, so to have a final image on where each of those reads maps on the query contig. Should i export the results in another format type than a txt ? I would like also to make this image visible somewhere in the web application.

Thank you.

   

blast alignment sequence • 1.5k views
ADD COMMENTlink modified 5.6 years ago by Pierre Lindenbaum127k • written 5.6 years ago by arronar200
2
gravatar for Pierre Lindenbaum
5.6 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum127k wrote:

Save as XML and transform to SVG using XSLT.

I wrote a stylesheet like this some times ago. See Blast Stylesheet

ADD COMMENTlink written 5.6 years ago by Pierre Lindenbaum127k

Thank you very much for the code. I would like to make you a question though.

I run it and in hits, it writes something like this : 2 - 268 near the e-value. What that means ? I noticed that either the hit is near the 5' end or 3' end it has such a small numbers.

E.g my target sequence is a 1434 bases long . One hit that seems to be near the 3' end, has this label : 3 - 272 (+) e=9.49817e-44 

while another one that is near the 5' end, has this label : 2 - 220 (+) e=5.94152e-36

So what these numbers means ?

Thank you.

ADD REPLYlink modified 5.6 years ago • written 5.6 years ago by arronar200
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