How does orthomclBlastParser output looks like

Question

[AP]

Hello everyone,

I am running Orthomcl in the set of proteomes I am working on and now I am in orthomclBlastParser step. The output that I got from blastp is in m-8 format as specified by the maual.

head blastp.out
T415|100119     HDV247|16147    100.000 136     0       0       1       136     1       136     6.24e-98        270
T415|100119     T415|100119     100.000 136     0       0       1       136     1       136     6.24e-98        270
T415|100119     F79|421682      99.265  136     1       0       1       136     1       136     1.39e-97        269
T415|100119     F109|816076     99.265  136     1       0       1       136     1       136     1.39e-97        269
T415|100119     F23|68052       99.265  136     1       0       1       136     1       136     1.39e-97        269
T415|100286     HDV247|16189    100.000 289     0       0       1       289     1       289     0.0     573
T415|100286     HDV247|16178    100.000 289     0       0       1       289     1       289     0.0     573
T415|100286     HDV247|16163    100.000 289     0       0       1       289     1       289     0.0     573
T415|100286     F79|421868      100.000 289     0       0       1       289     1       289     0.0     573
T415|100286     F105|44962      100.000 289     0       0       1       289     1       289     0.0     573

Now after I ran orthomclBlastParser I got the following output. If you see in column 5 and 6 looks like the e value is split up. I don't know if its supposed to be like that or not? I didn't get any error while running this though.

 head similarSequences.txt
T415|100119     HDV247|16147    T415    HDV247  6.24    -98     100     100
T415|100119     T415|100119     T415    T415    6.24    -98     100     100
T415|100119     F79|421682      T415    F79     1.39    -97     99.3    100
T415|100119     F109|816076     T415    F109    1.39    -97     99.3    100
T415|100119     F23|68052       T415    F23     1.39    -97     99.3    100
T415|100286     HDV247|16189    T415    HDV247  0       0       100     100
T415|100286     HDV247|16178    T415    HDV247  0       0       100     100
T415|100286     HDV247|16163    T415    HDV247  0       0       100     100
T415|100286     F79|421868      T415    F79     0       0       100     100
T415|100286     F105|44962      T415    F105    0       0       100     100

I searched but could not find the detail on output format of this orthomclBlastParser. Why are those column 5 and 6 (evalue) split up? and what are the headings for each column? Any input will be highly appreciated.

Thanks, Ambika

Answer 1

[GenoMax]

If you see in column 5 and 6 looks like the e value is split up.

Yes e-value is split into mantissa and exponent.

From code page:

output:
  tab delimited text file, with one row per query-subject match. the columns are:
     query_id, subject_id, query_taxon, subject_taxon,
     evalue_mant, evalue_exp, percent_ident, percent_match

[AP]

Thank you!!