Legacy Blastx Output (Karlin-Altschul Statistics) From Xml Output

Question

[random5823397]

If have to generate legacy blastx output from Blast XML output (why do people still require this!!!?). The legacy output has a block starting with

                                                             Score    E
Sequences producing significant alignments:                  (bits) Value  N

dbseq_1                                                           399   e-109  2
dbseq_2                                                           389   e-106  3

The parameters N is documented as follows:

Ungapped alignments and results from blastx and tblastn will have an additional column ('N'), displaying the number of different segment pairs used to produce the alignment, according to the Karlin-Altschul statistics.

I have no idea, how to get this value out of the Blast XML file. Can anybody help me? If not, this post is intended to clarify this issue for others in future.

[Pierre Lindenbaum]

Am I wrong ? I cannot find this parameter "N" in a blastx/XML.

<Hit>
  <Hit_num>1</Hit_num>
  <Hit_id>gi|348569288|ref|XP_003470430.1|</Hit_id>
  <Hit_def>PREDICTED: zinc finger CCCH domain-containing protein 7B-like [Cavia porcellus]</Hit_def>
  <Hit_accession>XP_003470430</Hit_accession>
  <Hit_len>1345</Hit_len>
  <Hit_hsps>
    <Hsp>
      <Hsp_num>1</Hsp_num>
      <Hsp_bit-score>44.669</Hsp_bit-score>
      <Hsp_score>104</Hsp_score>
      <Hsp_evalue>0.0149519</Hsp_evalue>
      <Hsp_query-from>231</Hsp_query-from>
      <Hsp_query-to>368</Hsp_query-to>
      <Hsp_hit-from>322</Hsp_hit-from>
      <Hsp_hit-to>373</Hsp_hit-to>
      <Hsp_query-frame>3</Hsp_query-frame>
      <Hsp_hit-frame>0</Hsp_hit-frame>
      <Hsp_identity>27</Hsp_identity>
      <Hsp_positive>30</Hsp_positive>
      <Hsp_gaps>6</Hsp_gaps>
      <Hsp_align-len>52</Hsp_align-len>
      <Hsp_qseq>VSREWGEAERTATH------LATA*WTVFSPQRLMERQRRKADIEKGLQFIQ</Hsp_qseq>
      <Hsp_hseq>LDEPWGKGWGRAGHRPALAVLLTDGLHALSLQRLMERQKRKADIEKGLQFIQ</Hsp_hseq>
      <Hsp_midline>+   WG+    A H      L T      S QRLMERQ+RKADIEKGLQFIQ</Hsp_midline>
    </Hsp>
  </Hit_hsps>
</Hit>
<Hit>

[random5823397]

I cannot find it either. I just wanted to make sure it is really not there.

[Pierre Lindenbaum]

"why do people still require this!!!?"=> ?

[random5823397]

I mean, why do programs depend on unstable text output instead of structured XML/ASN.1 or similar.