back in action / preSeq.pm

[Chris Dagdigian]

Hi folks,

Good to see everybody back in action on this list.

My makefiles for PreSeq and Parse work fine, the only thing I need to do is write some type of 
robust shell script called 'configure' that will do some quick in-place editing on PreSeq.pm and 
Parse.pm that will be able turn off/on the use of Parse.pm

Georg has metioned a bug in PreSeq and Steve C. has mentioned that he has made minor local 
additions to his copy of Preseq. If both of you folks could email me your info, I will 
incorporate the necessary changes into a new release.

Also- inside GI we have finally gotten around to replacing our numerous scripts that have been 
lying around for Blast/Fasta search result parsing. We now have a really nice object oriented 
Blast.pm module and the Fasta.pm will be done shortly. Both of these modules are quite 
standalone, capable of firing up a local or networked search and returning all kinds of 
different info raw or in various sorted ways. I was thinking that although these modules do not 
quite fit into our schema, they might be quite useful to the individual researcher.

One problem that was totally glossed over at the OIB meeting is that a majority of researchers 
out there do not have the support of bioinformatics groups containing dozens of computer 
scientists. While perl might not scale to super-industrial bioinformatics applications, there is 
a huge need for simple, robust tools that are useable by individuals. I really think that this 
is one area where BioPerl can be of tremendous help. Any thoughts?

regards,
Chris Dagdigian
cdagdigian@genetics.com