Scientific programs

LOHIRIA (by Jan Paces & Jakub Galgonek): Localization of High Identity Regions In Alignment. Program designed for helping with alergenic assesment (rules by WHO) or horizontal gene transfer (guidance by EFSA).
draw_chromosome_gc.pl (by Jan Paces): This program is in perl. It is designed for drawing pictures of gc profiles of long nucleotide sequences, e.g. whole chromosomes. This version needs to have installed perl (>5.0) with GD.pm module. Everything you need you can find at CPAN.
DicodonUsage (by Jan Paces): This set of perl scripts visualize dicodon bios in procaryotic genomes. It consist from count_dicodons.pl, which counts dicodons in given training set and two scripts dicodons.pl and dicodons_seq.pl, which draw dicodon preferences for six reading frames.
right handphyloMOD (by Simone Scalabrin): Perl script to compare orthologous sequences and extract putative regulatory regions. It is based on modular structure of regulatory regions and phylogenetic footprinting of orthologous sequences.

Jan Paces
Last modified: Thu Apr 7 15:20:46 CEST 2005
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