[Bioperl-l] Primer maps?

Marc Logghe Marc.Logghe at DEVGEN.com
Thu Feb 16 15:47:13 UTC 2006

Hi Mike,
Another route you might take is mapping your primers into
Bio::SeqFeature::Generic objects and add them to the seq object. Then
you dump the object into a rich sequence format like genbank and pass
that to EMBOSS's showseq application
Or you might do it completely with showseq. Here the only thing you need
is an annotation file containing the positions of the primers, followed
by any text (e.g. primer name).
Then you do:
showseq  <your seq file> -translate <cds_start>-<cds_stop> -format 4
-annotation <your_primer_file>
Have a look at http://emboss.sourceforge.net/apps/showseq.html for more

Marc Logghe, PhD
Expert Scientist Bioinformatics
deVGen NV
Technologiepark 30
B - 9052 Ghent-Zwijnaarde
Tel. +32 9 324 24 83
Fax. +32 9 324 24 25
Web: www.devgen.com

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	From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Michael Coyne
	Sent: Wednesday, February 15, 2006 10:20 PM
	To: bioperl-l at lists.open-bio.org
	Subject: [Bioperl-l] Primer maps?
	Hello all --
	I'm having a devil of a time figuring out how to make
restriction maps using BioPerl.  What I'm going for is output similar to
GCG's map program, but instead of using a set of defined restriction
enzymes, I'd like to use a set of primers, to create a primer map rather
than a restriction map.  I do not need a table of restriction enzymes
that cut or don't cut (or primers that match or don't match, in this
case), but an honest-to-goodness map, something like:
---------+---------+---------+---------+---------+---------+ 1980
	a                         M  E  I  V  S  T  F  D  E  L  Q  D  Y
	I also need translations of orfs, but I can use GenBank files as
input to the program and thus the CDS translations are already there, so
I'm guessing that shouldn't be too hard....  How does one create such a
map using the BioPerl modules?
	There are intriguing indications out there that such a thing is
possible (e.g. the Bio::Map:: * and Bio::Restriction:: * modules), but I
can't find a single example of code that creates such a basic,
bread-and-butter thing as a restriction map with orf translations.  The
documentation to these modules is fairly useless to me, consisting
mostly of internal methods and function prototypes.  Perhaps my skills
as a Perl programmer are to blame, but a clear example of how a map like
this is constructed would be a big help.
	Right now, I'm generating primer maps with system calls to
EMBOSS's remap, pointing it at a file of primer sequences rather than a
file of restriction enzyme sequences, but the results are less than
desired.  I'm considering trying to adapt tacg 4.1.0 or sequence
extractor 1.1 web-based code to my needs, but this seems like a lot of
work for an operation I suspect is possible in BioPerl.
	Any help greatly appreciated...

	 //=\   Michael J. Coyne                       phone: (617)
	 \=//   Channing Laboratory                    FAX:   (617)
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email:mcoyne at channing.harvard.edu
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