[Bioperl-l] Sequence Assembly:phrap to gap

Brian Osborne brian_osborne at cognia.com
Fri Jan 23 07:26:22 EST 2004


It sounds like you want something like phrap2gap. There's a version of this
available at the Sanger Centre but when I used this, some time ago, I had to
substantially modify because it read from particular Sanger databases.
Perhaps the phrap2gap's available now don't have these dependencies.


Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Anthony Underwood
Sent: Friday, January 23, 2004 4:42 AM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] Sequence Assembly:phrap to gap

Hi all,

I have a slightly off-topic question. I am assembling sequences using
the script phredPhrap which makes a .ace format assembly as well as a
phrap.out format assembly. I am using BioPerl to extract a lot of the
relevant information from the assembly however I would like to view the
assembly by converting it to a gap4 database, and using stadens gap4
viewer. Does anybody know of a script (perl or otherwise) that can
convert either the .ace or .out assembly to a gap4 database.

Many thanks,

Dr Anthony Underwood
Bioinformatics Group
Genomics, Proteomic and Bioinformatics Unit
Central Public Health Laboratory
Health Protection Agency
61 Colindale Avenue
t:    0208 2004400 ext. 3618
e: anthony.underwood at hpa.org.uk

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