A software detecting P element insertions

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A software detecting P element insertions

Postby alexandruecovoiu » Mon Mar 14, 2011 9:45 am

Dear drosphilists,

My name is Alexandru Al. Ecovoiu, I am a PhD drosophilist from Bucharest, Romania. My team is currently working on insertional mutagenesis with artificial P element derivatives. From our experience, is not quite a simple task to find out the precise site of insertion when a specific sequence is investigated. On-line BLAST or BLAT do not recognize explicitly parts of P elements as pertaining to the fly genome, so a little bit of work should be done manually. In order to help drosphilists working in such area we developed, in a collaboration with computer scientists, a new bioinformatics tool. It is named Genome ARTIST and it is able to find out, in a fast, direct manner, the exact site of a P insertion, its orientation relative to the afected gene, or the genes flanking the insertion. It is also usable for any other sequence homollgy search against Drosophila genome. For the moment, it is available only for UBUNTU LINUX, but we are working to develop versions for other platforms also. We would be honored if you would find Genome ARTIST to be be useful for your work. Reporting bugs and any other feed-back would be very helpful. The Genome ARTIST is a free software and it may be downloaded along with the pdf manual from http://www.bio.unibuc.ro/index.php?opti ... Itemid=105 The software already contains the preloaded 5.26 D.melanogaster genome, as it is designed to work off-line. Anyway, other genomes may be loaded, according to the manual instructions. At this moment only P{lacW} construct is preloaded in the database, but you may change it at will with P{EP} or other favorite transposon. Hoping that our work may represent a modest contribution to the Drosophila endeavor, we are waiting for your opinions or questions. Just in case, my address is alexandruecovoiu@yahoo.com
Please receive my best regards,

Alex
alexandruecovoiu
 
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