[Bioperl-l] WUBLASTP parsing problem

[Angshu Kar]

Hi,

Does WU-BLASTP has got something to do with the length of the
sequence names (or the sequence names)?
What is happening here is I use fasta format proteins to build the
blast (I do a distributed blastp) report. But when I parse the
report (using bioperl), the query column remains empty for some
results as :

*     328857    6.6e-135
     325331    6.3e-114
     325329    1.0e-113
     325332    1.7e-113
     325330    2.7e-113
.
.
*.

  while for some its perfect as:

*267750    280003    7.5e-301
267750    348279    7.5e-301
267750    345867    2.0e-300
267750    251915    2.0e-300
267750    346539    6.7e-300
.
*.
.

Some of my sequences are as:
*IMGA|AC159872_38.1 hypothetical protein AC159872.12 35121-35051 H
EGN_Mt050401 20060209 TIGR 1671.m00013
mrsciilhnmivederdtyaqrwtefeqpggngsstpqpystelrdpdvhhklqtdlvkh
iwikfgmyrd*
*
And part of the blastp (the one where I'm facing the issue) result
is as:

*Smallest
*
*  Sum
                                                               High
Probability
Sequences producing High-scoring Segment Pairs:              Score
P(N)      N

gi|33333045|gb|AAQ11687.1| MADS box protein [Triticum aes...  1318
6.6e-135  1
gi|47681327|gb|AAT37484.1| MADS5 protein [Dendrocalamus l...  1120
6.3e-114  1
gi|47681331|gb|AAT37486.1| MADS7 protein [Dendrocalamus l...  1118
1.0e-113  1
gi|47681325|gb|AAT37483.1| MADS4 protein [Dendrocalamus l...  1116
1.7e-113   1
gi|47681329|gb|AAT37485.1| MADS6 protein [Dendrocalamus l...  1114
2.7e-113  1
gi|47681323|gb|AAT37482.1| MADS3 protein [Dendrocalamus l...  1114
2.7e-113  1
11674.m04224|LOC_Os08g41950|protein K-box region, putative     976
1.1e-98    1
gi|28630961|gb|AAO45877.1| MADS5 [Lolium perenne]              967
1.0e-97   1
gi|44888605|gb|AAS48129.1| AGAMOUS LIKE9-like protein [Ho...   964
2.1e-97   1
11674.m04223|LOC_Os08g41950|protein K-box region, putative     899
1.6e-90    1
gi|34979580|gb|AAQ83834.1| MADS box protein [Asparagus of...   875
5.8e-88   1*

Could you please let me know if I'm missing something? Has the gi got to do
anything with this?

Thanking you,
Angshu