Gapped alignment display in Blixem

John Peden j.peden at oxagen.co.uk
Tue Oct 9 09:57:48 EST 2001


Dear Developers,

I downloaded binaries for acedb 4.9f and 4.9a (Alpha Binaries from
/pub/acedb/SUPPORTED).

I am using xace FMAP display to visualise gapped blast HSPs against a
60Kb BAC. I use the inbuilt blixem Blixem_N method to display the
gapped alignments, however I have found a problem with displaying
gapped results in the blixem viewer if the match lies outside the
first 20,700 or so of the BAC.
 

If the coordinates lie within the first 20,700 the display looks
normal.

e.g.
Sequence "Consensus"
Homol DNA_homol BE113399 EM_EST 1447 19001 19481 44 455 Align 19001 44


However if the coordinates of match on the subject are above 21Kb i.e.

Sequence "Consensus"
Homol DNA_homol BE113399 EM_EST 1447 21001 21481 44 455 Align 21001 44

The EST sequence is represented by dots ................ i.e. where
the nucleotides had been previously only gap characters are visible.
Note, all I do is change the self coordinates, if I select the
sequence I can still retrieve the original sequence object.


If I change to ungapped mode by removing the Align part of the model
i.e.

Sequence "Consensus"
Homol DNA_homol BE113399 EM_EST 1447 21001 21481 44 455 

Then the ungapped alignment is displayed i.e the sequence of the
aligned EST is visible.

Any thoughts about where this bug might be in the code, I couldn't
find anything obvious on the mailing list.

I believe it is something to do with the default "whole" window you
get when you launch blixem from within FMAP which seems to be approx
20.7kb.


Thanks 
  John

Computational Biology Group,
Oxagen Ltd, 91 Milton Park, Abingdon, OX14 4RY,
United Kingdom, Tel. +44 (0)1235 443384 Fax. +44 (0)1235 443301







John Peden,
Computational Biology Team Leader,
Oxagen Ltd, 91 Milton Park, Abingdon, OX14 4RY,
United Kingdom, Tel. +44 (0)1235 443384 Fax.  +44 (0)1235 443301





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