erratum: [Bioperl-l] StandAloneBlast -> bl2seq case

Marcel van Batenburg
Mon, 15 Oct 2001 15:58:57 +0200 (MET DST)

Dear group,

The executable is blastn which is called by bl2seq.


On Sat, 13 Oct 2001, Marcel van Batenburg wrote:

> Dear group,
> I downloaded the package bioperl (the version before the last
> version), for I'm interested of using some bioperl modules. 
> By the way I'm working on an operating system called Solaris. 
> This system is used by more people, so I have not yet installed
> the bioperl modules in general perl directories.
> I'm employing your package to align one dna sequence of fixed length
> with other sequence using blast. I used the executable bl2seq. How can
> one run this executable in a loop (so more than once) without 
> being stopped by EXCEPTION message, and how can one align a dnasequence
> with less than 11 nucleotides without being confronted with the
> same EXCEPTION message? 
> The bl2seq could align a dnasequence with less than
> 11 consequtive nt when one makes a dna sequence of 11 nt by adding to its
> flanks, IUPAC symbol N. The module could give me all possible 
> sequences. Subsequently, one loops thru these sequences when aligning 
> to a fixed second dnasequence. This will work if the excutable does not
> terminate the holy workings of my perl script due to a detected 
> misalignment (alignment is according to bl2seq an aligment of more than/or
> equal to 11 consecutive basepairs).
> Another solution is also welcome.
> I'm looking forward to your reply,
> Marcel
> P.S. Hopefully, I will never see any if-then-else-if statements. Gosh, A
>      true object-oriented code should handle the choices of the user via
>      its data structure.
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