Research

Automatic Detection of Phylogenetic Footprints

Abstract

Unusually high conservation/similarity of non-coding sequence fragments is thought to indicate functionality. As far as non-coding sequence is concerned, the most common function of DNA is to bind proteins. Therefore, conserved regions are usually regulatory regions.
Our program TRACKER detects multiple local alignments most efficiently in large homologous gene clusters of not to closly related species. In this case the tracker hits are termed 'cliques' and resemble phylogenetic footprint clusters with an average length of 15-300nt.



Input and Output




INPUT		Uses sequences of 2 to very many large, homologous regions and the gene positions (to exclude genes).
OUTPUT		A big list of footprints containing there position and length in the sequences [latex]. A postscript overview. Dialign alignements of all individual footprint (cluster).




Download Tracker

Tracker can not be downloaded yet. See below for resons.



Countdown to the Online Availability of Our Program

• Tracker is not running on Windows yet
• Writing the input files is a bit complicated and has to be changed
• Usefull error messages have to be included
• Conversion into a web tool is going to be initiated



Other Usefull Tools

Cutter		Sequence manipulation tool, also cuts exonfiles
genbank2exons		writes an exonfile using the information in a genbank file
proc_dialign		produces a nice postscript overview of a dialign alignment




BlastZ

blastz