[Bioperl-l] Sequence Assembly:phrap to gap

Cook, Malcolm MEC at Stowers-Institute.org
Fri Jan 23 14:14:06 EST 2004

You might consider getting gcphrap
(http://www.mrc-lmb.cam.ac.uk/pubseq/phrap.html) from which I quote:

"The gcphrap command works in much the same way as the standard Phrap
command. Indeed as it is the same source code, it is just the input and
output formats which will differ. The key difference is that gcphrap
automatically detects the difference between a file containing fasta
sequences and a file containing a list of Experiment File filenames. The
extra "-exp" option may be used (regardless of input format) to output
the assembly as a series of Experiment Files suitable for assembly into
Gap4 using the "Directed Assembly" option. For example: 

	$ gcphrap seqs_fasta.screen -exp efiles > phrap.out

The above command will produce a directory named efiles containing one
Experiment File per sequence. These Experiment Files have 'AP' lines
added to them to define the assembly positions. 


-----Original Message-----
From: Anthony Underwood [mailto:theunderwoods at clara.co.uk] 
Sent: Friday, January 23, 2004 3:42 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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