[Bioperl-l] (repost) virtual gel from chromatogram, staden library on Windows

[Remo Sanges]

>One of our investigators wants to create virtual
>sequence gels from ABI chromatogram files.
>While I remain unconvinced regarding the merits
>of this idea, meanwhile I'm trying to determine
>feasibility.

>I found that ABI.pm in the BioPerl distribution
>requires a Staden library at:
>ftp://ftp.mrc-lmb.cam.ac.uk/pub/staden/io_lib/

>I would like to come up with a Windows or
>Windows/Linux solution to the original problem
>if practical,
>but would settle for a Linux-only solution,
>especially because I can probably turn this into
>web application.

So I think you can try to use phred www.phrap.org
in order to extract sequences from ABI files in
fasta format and than use Bio::Seq::fasta to
manage them.
It works fine on Linux and is constantly developed
while, if I well remember, Staden package is no
longer supported from last month.

Remo

_____________________________________
Remo Sanges - Ph.D. Student
BioGeM - IGB
Gene Expression & Sequencing Core Lab
Via Pietro Castellino 111
80131 Naples - Italy
Tel:+390816132303 - Fax:+390816132262
sanges at biogem.it - sanges at iigb.na.cnr.it
_____________________________________