[Gmod-ajax] blast to jbrowse track

[Michał T. L. <m.t...@gm...>]

Hi all,
I ran tblastn and have got this Blast output:






















*NIATv7_g23718.t1        NbV1Ch10        95.789  95      4       0
596     690     12945534        12945818        2.55e-49
 193NIATv7_g23718.t1        NbV1Ch10        70.290  138     4       1
473     573     12943183        12943596        9.76e-46
 182NIATv7_g23718.t1        NbV1Ch10        70.290  138     4       1
472     572     12943180        12943593        1.36e-44
 179NIATv7_g23718.t1        NbV1Ch10        97.561  41      1       0
122     162     12937586        12937708        1.02e-29
 85.5NIATv7_g23718.t1        NbV1Ch10        93.939  33      2       0
  91      123     12937413        12937511        1.02e-29
 70.9NIATv7_g23718.t1        NbV1Ch10        91.111  45      4       0
  435     479     12942868        12943002        1.14e-28
 84.7NIATv7_g23718.t1        NbV1Ch10        100.000 31      0       0
  405     435     12942669        12942761        1.14e-28
 67.8NIATv7_g23718.t1        NbV1Ch10        97.500  40      1       0
  171     210     12938519        12938638        4.58e-16
 87.8NIATv7_g23718.t1        NbV1Ch10        81.818  11      2       0
  161     171     12938374        12938406        4.58e-16
 22.3NIATv7_g23718.t1        NbV1Ch10        83.333  48      8       0
  271     318     12939766        12939909        2.79e-15
 86.7NIATv7_g23718.t1        NbV1Ch10        94.737  38      2       0
  33      70      12931492        12931605        2.30e-13
 80.5NIATv7_g23718.t1        NbV1Ch10        82.857  35      6       0
  251     285     12939588        12939692        5.41e-09
 66.2NIATv7_g23718.t1        NbV1Ch10        100.000 31      0       0
  317     347     12940034        12940126        1.12e-08
 65.1NIATv7_g23718.t1        NbV1Ch10        96.970  33      1       0
  1       33      12931031        12931129        1.22e-08
 65.1NIATv7_g23718.t1        NbV1Ch10        75.000  40      10      0
  336     375     12940960        12941079        1.07e-07
 62.0NIATv7_g23718.t1        NbV1Ch10        100.000 29      0       0
  223     251     12938772        12938858        3.82e-07
 60.1NIATv7_g23718.t1        NbV1Ch10        95.652  23      1       0
  70      92      12932440        12932508        0.014
45.1NIATv7_g23718.t1        NbV1Ch01        80.000  60      12      0
473     532     135384227       135384048       2.25e-37
 96.3NIATv7_g23718.t1        NbV1Ch01        82.692  52      9       0
  529     580     135383956       135383801       2.25e-37
 85.9NIATv7_g23718.t1        NbV1Ch01        92.683  41      3       0
  122     162     135393270       135393148       1.89e-27
 82.8NIATv7_g23718.t1        NbV1Ch01        90.625  32      3       0
  92      123     135393437       135393342       1.89e-27
 65.5NIATv7_g23718.t1        NbV1Ch01        73.626  91      20      3
  595     682     135374896       135374627       1.62e-22
 110NIATv7_g23718.t1        NbV1Ch01        72.500  40      11      0
31      70      135399457       135399338       7.51e-21        67.8*

Next, I ran the below command which is part of BioPerl in order to generate
a gff3 file for Jbrowse:

*bp_search2gff.pl <http://bp_search2gff.pl> --in all-tblastn.1000.out --out
all-tblastn.gff3 --version 3 -f blast --match --source tBLASTn.NitVsNb
--type hit*

However, the command has generated an empty file. Did I use command wrongly
or is there another way to add Blast tracks to JBrowse?

Thank you in advance,

Michal