[Bioperl-l] EST Alignment questions

[Jamie Hatfield]

> From: Heikki Lehvaslaiho [mailto:heikki@ebi.ac.uk] 
> 
> Jamie, thanks for your help on the reverse translate problem!

Haha, I was just joking around.  I just wanted to justify my "right" to
post a question with the fact that I had answered one.  It was a small
task, and nothing compared to those of you who practically make it your
job to maintain this awesome project.  Mega-kudos to all of you.
(Lstein, Heikki, Jason Stajich, Hilmar, Ewan, etc... Those are the names
I keep seeing as I scroll through the archives looking for answers to
questions along my areas of interest.  Please, no flames for those I
left out!!)  That being said, I'll add my occasional, meager
contribution when I can.  :-)

> The "typical"  use of SimpleAlign is to store and manipulate results
> from a MSA prograom like ClustalW. Hope this helps to understand where
> SimpleAlign comes from.

Yes, I understand that is the use and origin of SimpleAlign.  I was just
trying to twist it to my use.

> There is a group of modules in Bio::Coordinate that might be of use.
> They do not deal with sequences but in coordinate systems. 
> You could use
> Bio::Coordinate::Collection to store the start and end of ESTs (or
> subranges of them) and how they map to the consensus. 
> 
> The key function is map() which can tell you where in the consensus
> sequence any range in any of the ESTs it is, or the other way 
> round you
> can get back a all the overlapping ESTs and their ranges in EST
> coordinates. If you change the consensus, you can use the first
> collection to create a new one.

That seems to make sense.  I've downloaded the Coordinate tar and got it
working, but apparently I have a (rather) old version of bioperl because
Location::Simple doesn't accept seq_id (instead it looks for seqid).
Seeing as I'm not sysadmin, I'm gonna get him to dl the newest version
and we'll explore more from there.

Coordinate mixed with Location::Split seems to be the way to go with
this, Though we'll see after more experimentation.

Thanks!

------------------------------------------------------------------------
-
Jamie Hatfield                                Room 541H, Marley Building
Systems Programmer                            University of Arizona
Arizona Genomics Computational                Tucson, AZ  85721
  Laboratory (AGCoL)                          (520) 626-9598