[Genome] BLAT gives wrong tStarts for translated searches.

[Kevin M. Carr]

Hello all,

I am attempting to align RefSeq mRNA sequences from related species to an
in-house draft genome assembly.  I am doing the alignment in protein space
with the -t=dnax and -q=rnax.  While the results for alignments to the +
strand appear normal I am getting incorrect (or at least confusing) output
for alignments to the - strand of the target.  More specifically the
individual tStarts locations do not fall within the T start and T end
positions given.  Here is and example:

psLayout version 3

match   mis-    rep.    N's     Q gap   Q gap   T gap   T gap   strand  Q
Q       Q       Q       T               T       T       T       block
blockSizes       qStarts  tStarts
        match   match           count   bases   count   bases           name
size    start   end     name            size    start   end     count
----------------------------------------------------------------------------
----------------------------------------------------------------------------
-------
442     122     0       0       3       951     3       846     +-
SINFRUT00000182842      1599    78      1593    stig_26 225935  221426
222836  4       180,228,36,120,  78,288,552,1473,
3099,3330,3585,4389,

As can be seen, the T start is 221426 and T end is 222836 but the tStarts
are given as 3099,3330,3585,4389

It seems that every alignment to the - strand is incorrect while every one
to the + strand seems fine.  I have run this using command line BLAT (32X1)
and gfServer/gfClient (33X7) (gfServer started with -trans and gfClient run
with -q=rnax) and the results are the same either way.

Am I missing something?

Insights and suggestions greatly appreciated.
 
Kevin M. Carr

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Research Technology
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Michigan State University
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