i-ADHoRe 3.0 – Detect Degenerated Genomic Homology

i-ADHoRe 3.0

:: DESCRIPTION

i-ADHoRe is a highly sensitive software tool to detect degenerated homology relations within and between different genomes.

::DEVELOPER

Van de Peer Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Perl

:: DOWNLOAD

i-ADHoRe

:: MORE INFORMATION

Citation

i-ADHoRe 3.0–fast and sensitive detection of genomic homology in extremely large data sets.
Proost S, Fostier J, De Witte D, Dhoedt B, Demeester P, Van de Peer Y, Vandepoele K.
Nucleic Acids Res. 2012 Jan;40(2):e11. doi: 10.1093/nar/gkr955.

Simillion, C., Janssens, K., Sterck, L., Van de Peer, Y. (2008)
i-ADHoRe 2.0: An improved tool to detect degenerated genomic homology using genomic profiles.
Bioinformatics 24, 127-8.

HYDEN – A software for Designing Degenerate Primers

HYDEN

:: DESCRIPTION

HYDEN (HighlY DEgeNerate primers) is a program for designing pairs of degenerate primers for a given set of DNA sequences. HYDEN works well for large input sets of genomic sequences (e.g., hundreds of sequences of length 1Kbp).

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

Windows/Linux

:: DOWNLOAD

HYDEN

:: MORE INFORMATION

Citation

Degenerate primer design: theoretical analysis and the HYDEN program.
Linhart C, Shamir R.
Methods Mol Biol. 2007;402:221-44.

DEODAS 0.2.0 -DEgenerate Oligo Nucleotide Design & Analysis System

DEODAS 0.2.0

:: DESCRIPTION

DEODAS designs & analyzes consensus-degenerate oligonucleotide probes for biological research. DEODAS automatically designs and screens, probes against databases of known genes & stores the information in a searchable database.

::DEVELOPER

Karl Diedrich

:: SCREENSHOTS

:: REQUIREMENTS

Linux
gtkmm, available at http://gtkmm.sourceforge.net/
libsigc++, available at http://libsigc.sourceforge.net/
python
pygtk
pygnome
postgresql