[Bioperl-l] Primer maps?
heikki at sanbi.ac.za
Thu Feb 16 12:32:51 EST 2006
Marc's suggestion is the best I've heard.
We really do not have any kind of pretty print functionality within BioPerl.
I guess there has not been a pressing need. Bio::Graphics has filled in the
need for sequence display.
I think Bio::Seq::PrettyPrint could be a great way to design prettyprinting in
very modular way so that it can print out anything mapped to a sequence
location. The EMBOSS showseq would be a great help in there. A student
Would anyone be interested?
On Thursday 16 February 2006 17:47, Marc Logghe wrote:
> 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)
> //=\ EBRC, Room 617
> \=// 221 Longwood Avenue
> email:mcoyne at channing.harvard.edu
> //=\ Boston, MA 02115 mjcoyne at comcast.net
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______ _/ _/_____________________________________________________
_/ _/ _/ Heikki Lehvaslaiho heikki at_sanbi _ac _za
_/_/_/_/_/ Associate Professor skype: heikki_lehvaslaiho
_/ _/ _/ SANBI, South African National Bioinformatics Institute
_/ _/ _/ University of Western Cape, South Africa
_/ Phone: +27 21 959 2096 FAX: +27 21 959 2512
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