From G.Fletcher at mailbox.gu.edu.au Thu Mar 29 18:12:23 2001 From: G.Fletcher at mailbox.gu.edu.au (Gordon Fletcher) Date: Wed Aug 4 23:58:54 2004 Subject: [BNE-PM] A Welcome Message-ID: Hello to all the new members to the group over the recent weeks. I thought it might be appropriate to send a _short_ message as the traffic on the list has been extremely quiet of late. Although I suspect that this is partly a result of the extra security that pm.org has placed on the list I keep getting asked to approve spam from Indian micro-electronics companies! For those of you who are new perhaps posting a quick bio of yourself and your interests would help everyone know who's around. The list is always open to suggestions - actual meetings and other activities that might be Perl oriented. The forum is open - we're all listening (so to speak). Gordon From fc at maths.uq.edu.au Thu Mar 29 19:07:34 2001 From: fc at maths.uq.edu.au (Francis Clark) Date: Wed Aug 4 23:58:54 2004 Subject: [BNE-PM] A Welcome In-Reply-To: Message-ID: ok - hello perl mongers - my name is Francis and I am a computational biologist... Most of my work involves playing with large text files, for which I find PERL superb. My two major projects are: 1. spliced alignments of genomic and transcript data The genes of things like humans (in fact, most things above bacteria) contain streches of sequence (called introns) that do not code for protein. After the gene is copied from the DNA into an RNA copy, a machine called the spliceosome splices out (removes) the introns. (see diagram) DNA ============================================================== (genomic seq) RNA copy 111111111-------------22222222222------------33333333333 of gene exon 1 intron 1 exon 2 intron 2 exon 3 mRNA 1111111112222222222233333333333 (transcript seq) This mRNA (messenger RNA) is now used as the recipe to make a protein. There exist large data sets of both gene sequence and transcript sequence (fragments of mRNAs), although these are not matched up with eachother. By using sequence matching software (BLAST) it is possible to match up transcript sequences with genomic sequence. By constructing such 'spliced alignments' it is possible to: a) find genes b) determine the intron / exon structure of genes c) observe that many genes have more than one pattern of splicing, and thus are able to produce more than one protein from a single gene. Apart from the sequence alignments, which are generated with BLAST, all of the data analysis and management is done using perl. One day I'll learn about databases, but I reckon that big fat text files and perl are doing just fine. 2. Hunting mobile elements in genomic sequence The genomes of things like humans are mostly non gene sequence. What is all this 'other DNA'? Is it junk? packaging? important, but of unknown function? We do, however, know how most of it got there. Mobile elements (including things like retroviruses) are genomic 'parasites'. They get into genomes, and make copies of themselves everywhere. When these elements get into the germ line, they become part of the genome. Perhaps half of the human genome is made up of the corpses (in varying states of decay) of such mobile elements. It is thought that most of the mobile elements in human are dead, although mouse is full of live stuff. Once again, BLAST makes it possible to identify regions of homologous sequence within a (partial) genome, and using PERL I am able to sort through all this data and find patterns of homology indicative of various classes of mobile element. BLAST, big text files and PERL - superb. Anyway, I didn't mean to go on... for anyone who makes it to here... I'd be interested to hear from anyone does similar things. Francis -- Francis Clark, Department of Mathematics and Institute for Molecular Bioscience University of Queensland, Australia. On Fri, 30 Mar 2001, Gordon Fletcher wrote: > > Hello to all the new members to the group over the recent weeks. > > I thought it might be appropriate to send a _short_ message as the > traffic on the list has been extremely quiet of late. Although I suspect > that this is partly a result of the extra security that pm.org has placed > on the list I keep getting asked to approve spam from Indian > micro-electronics companies! > > For those of you who are new perhaps posting a quick bio of yourself and > your interests would help everyone know who's around. > > The list is always open to suggestions - actual meetings and other > activities that might be Perl oriented. > > The forum is open - we're all listening (so to speak). > > Gordon > > From stuart.murnain at qca.org.au Thu Mar 29 19:49:31 2001 From: stuart.murnain at qca.org.au (Stuart Murnain) Date: Wed Aug 4 23:58:54 2004 Subject: [BNE-PM] A Welcome Message-ID: <150AA6FD0325D21180B7006094572CC71ED5E5@SERVER> Hello fellow perl-mongers, My name is Stuart. I work at the Queensland Competition Authority. I use Perl for cgi and asp, sys admin type tasks and database manipulation. I recently got some work munging futures transactions into various time series with Perl. Nice to see some activity on the Brisbane perl mongers list :-) Regards, Stu. -------------------------------- Stuart Murnain IT Officer Queensland Competition Authority Level 19, 12 Creek St Brisbane QLD 4000 Phone: (07) 3222 0528 Fax: (07) 3222 0599 stuart.murnain@qca.org.au -------------------------------- ------------------------------------------------------------- The information contained in this message and any annexure is confidential and intended only for the named recipient(s). If you have received this Email in error, please notify us immediately by return email or telephone +61 7 3222-0555 and destroy the original message. Please note that if you are not the intended recipient, no part of this message may be reproduced, adapted or transmitted. Emails may be interfered with, may contain computer viruses or other defects and may not be successfully replicated on other systems. We give no warranties in relation to these matters. 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