Downloads

OligoWords

This standalone cross platform Python program calculates the various oligonucleotide usage statistical parameters seen in the Genome Browser. Requires the Python programming language and a genome file in fasta (.fst, .fas or .fna) or GenBank (.gbk) format. Example sequence files available for download.

Download (for Windows, 5MB)
Download (for Linux, 2MB)
Download (for Mac, 2MB)
Download (source Python files, 13KB)
Download (example sequence files, 0.9MB)

SeqWord Viewer

Download to analyse your own genomes locally (with data from OligoWords). Results are displayed in a browser window. Requires Java 1.5 and up. The HTML-embedded Java-applet to be used in any compatible web-browser. (It has been tested on openSUSE 10.2, Gentoo Linux 2.6, Fedora Core 5 and Microsoft Windows XP workstations using Microsoft Internet Explorer 6.0, Maxthon 1.5.9, Mozilla Firefox 2.0, Mozilla SeaMonkey 1.1.1, Safari 3.0.4 for Mac, Konqueror 3.5.5 and 3.5.7, and Opera 9.10 browsers with Java 1.5)

Download (SeqWord_Viewer, 0.9MB)

SeqWord Sniffer

This program was developed to perform an automatic search in genomic DNA for horizontally transferred genomic elements.

Download (SWGIS_1.0.zip 2012.04.26, 9.8MB - compatible with all OS where Python 2.5 is installed).

LingvoCom

This program was developed to perform analysis and visualization of intrinsic phylogenetic and donor-recipient links between genomic islands and their host chromosomes.

Download (LingvoCom_1.0.zip 2012.04.26, 2.7MB - compatible with all OS where Python 2.5 is installed, SVG images may be viewed in Mozilla Firefox (the best) or Chrome).

SeqWord OligoDBViewer

The databases of signature oligonucleotides from 8 to 14 bp may be edited and searched for the most specific words to discriminate between bacterial taxa. A GUI and a number of pre-calculated databases are available for download:
 

OligoDBViewer.zip for Python 2.5.4		7.02 Mb
DATABASES:
bacteria	892 genomes	142 Mb

SeqWord MetaLingvo

 MetaLingvo program was developed for:

• Linguistics analysis and visualization of genome DNA sequences;
• DNA sequence clustering by similarity of oligonucleotide frequency patterns;
• Alignment free phylogenomic study;
• Binning of unknown DNA sequences and metagenomic DNA reads to taxonomic units;
• Creation of user databases of genome specific oligonucleotide usage patterns;

basing on analysis of frequencies of oligonucleotides – oligonucleotide usage patterns (OUP).