grouping hsps in btab format

[Chris Hemmerich]

Hello,

Does the btab format retain the information to group hsps that have been
combined to generate an E-value beyond assuming consecutive, identical
hsps are grouped? We're looking a transcriptome data and could have
millions of hsps per pipeline, so I'm hesitant to automate an assumption.

BioPerl provides an 'n()' method fo HSPs that resolves this unambiguously.
I'm considering sticking it in the empty column 15 "segment_number" in our
local blast2btab.pl or adding a new column at the end. Does anyone have a
better idea for handling this? Does anyone care enough to commit a
consistent method of doing it to svn?

Cheers and Thanks,
  Chris

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[Joshua Orvis]

Chris -

I think using that column would be appropriate for this need.  In fact, another component had a similar need to group alignment sections and set the initial use here (see the documentation for aat_aa within Ergatis.)  It actually used two values, chain ID along with segment number, to group different alignment segments or HSPs.  I think chain ID is the more appropriate term here, if we want to be consistent.  The segments were just increasing integers within each chain.

Joshua

On Sun, Mar 25, 2012 at 9:06 PM, Chris Hemmerich <[hidden email]> wrote:

Hello,

Does the btab format retain the information to group hsps that have been
combined to generate an E-value beyond assuming consecutive, identical
hsps are grouped? We're looking a transcriptome data and could have
millions of hsps per pipeline, so I'm hesitant to automate an assumption.

BioPerl provides an 'n()' method fo HSPs that resolves this unambiguously.
I'm considering sticking it in the empty column 15 "segment_number" in our
local blast2btab.pl or adding a new column at the end. Does anyone have a
better idea for handling this? Does anyone care enough to commit a
consistent method of doing it to svn?

Cheers and Thanks,
 Chris

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