CpG programs

Rodrigo Lopez rls at ebi.ac.uk
Mon Dec 22 10:19:43 UTC 2003


Sorry for the late reply. I'm currently re-writing a small portion of the
code to speed things up together with a collaborator. As soon as this one is
tried and tested we will move to replace the old version of newcpgreport
with this one. As soon as that is done a name change from newcpgreport to
cpgreport will be requested and the old programs can be retired.

Thanks and Merry Xmas to all!!!!


> -----Original Message-----
> From: owner-emboss-dev at hgmp.mrc.ac.uk
> [mailto:owner-emboss-dev at hgmp.mrc.ac.uk]On Behalf Of Gary Williams, Tel
> 01223 494522
> Sent: 12 December 2003 13:59
> To: emboss-dev at embnet.org
> Subject: CpG programs
> EMBOSS has several programs for finding CpG islands:
> cpgreport	Reports all CpG rich regions
> newcpgseek	Reports CpG rich regions
> newcpgreport	Report CpG rich areas
> The documentation (originally supplied by the author) says that for all
> practical purposes you should probably use newcpgreport.
> There is probably a case for retiring some of these programs to the
> 'make check' section of the Makefile? (i.e remove them from the standard
> distribution unless explicitly compiled.)
> Which of these, if any, do you use and why?
> Regards,
> Gary
> --
> Gary Williams
> MRC Rosalind Franklin Centre for Genomics Research
> Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
> Tel: +44 1223 494522			Fax: +44 1223 494512
> E-mail: gwilliam at rfcgr.mrc.ac.uk	Web: http://www.rfcgr.mrc.ac.uk

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