[Bioperl-l] Regarding blast in Bioperl

Robert Bradbury robert.bradbury at gmail.com
Sat Jan 9 14:52:53 EST 2010


Roopa,

Mark is correct, you have to be very careful of single vs. double quotes in
perl. Double quoted strings are "interpreted" while single quoted strings
are taken literally is my current understanding.

I tried to run your script (with fixes) but without the supporting files it
appears to be impossible.

What I am curious about is what it is trying to do, I was particularly i
particularly intrigued by some apparent efforts to parse blast results into
color enhanced HTML and without thinking about the code in detail it seems
easier to simply ask what you are trying to do?  I find "classical" blast
results particularly tedious and long for blast results that display concise
information as the NCBI homologene cross-species comparisons do.
Unfortunately NCBI has deemed their methods (I have asked them) "too complex
to disclose (for a person comfortable in dealing with assembly language, or
even gate level electronics -- "too complex" is a very relative concept)".
One has the option of using NCBI with a limited number of species but good
display methodologies or Ensembl with many more species but less desirable
display methodologies (phylogenetic tree derived from cross species
comparisons).  And for the WRN protein which may play a key role in aging
(through the activity of its exonuclease domain mutating DNA sequences and
inducing microdeletions and microinsertions this gets important because it
appears that the *C. elegans* genome is missing the exonuclease domain (so
it may be useless from the perspective of studying aging), and the other 4
nematode species which have been sequenced aren't even in the NCBI nor the
Ensembl databases.  Needless to say, if we manage in the near future, given
the drop in sequencing costs, to sequence the nematodes which are
freeze/thaw tolerant (which induces DSB that have to be repaired) those
genomes will be unlikely to be in the NCBI/Ensembl databases either.  So
there is a requirement for the user to develop the ability to mix and match
public and obscure databases in creative ways to provide easy to interpret
information.

Robert Bradbury


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