CAT / Xat 0.8.6 – Cross-species Alignment Tool

CAT / Xat 0.8.6

:: DESCRIPTION

 CAT (Xat) is designed to be a cross-species (both intra-species and inter-species), nucleotide level, cDNA-to-genome alignment software. It uses improved heuristics to effectively balance specificity, sensitivity and speed, and is optimized for genome-wide mapping.

::DEVELOPER

CAT team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 CAT / Xat

:: MORE INFORMATION

Citation

A cross-species alignment tool (CAT).
Li H, Guan L, Liu T, Guo Y, Zheng WM, Wong GK, Wang J.
BMC Bioinformatics. 2007 Sep 19;8:349.

GATA 0.7 – Graphic Alignment Tool for Comparative Sequence Analysis

GATA 0.7

:: DESCRIPTION

GATA is a stand alone, platform independent, graphic alignment tool for comparative sequence analysis. It makese use of BLAST to graphically align two DNA sequences creating box-line-box representations of window scored local alignments. Gata can also display extensive gene annotation using a standardized GFF format.

::DEVELOPER

Eisen Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

 GATA

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2005 Jan 17;6:9.
GATA: a graphic alignment tool for comparative sequence analysis.
Nix DA, Eisen MB.

HAXAT 1.04 – Homopolymer Aware Cross Alignment Tool

HAXAT 1.04

:: DESCRIPTION

HAXAT uses a novel dynamic programming algorithm for solving the optimal local alignment between a 454 nucleotide and a protein sequence by allowing frame-shifts, guided by 454 flowpeak values.

::DEVELOPER

IFM Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 HAXAT

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Sep 12;13:230. doi: 10.1186/1471-2105-13-230.
Highly improved homopolymer aware nucleotide-protein alignments with 454 data.
Lysholm F.

SRmapper 0.1.5 – Genome-hashing Alignment tool

SRmapper 0.1.5

:: DESCRIPTION

SRmapper is a tool for aligning short reads obtained from next-generation sequencing experiments to a reference genome.

::DEVELOPER

Wong Group

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/ MacOsX/Windows
  • C++ Compiler

:: DOWNLOAD

 SRmapper

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Feb 1;29(3):316-21. doi: 10.1093/bioinformatics/bts712. Epub 2012 Dec 24.
SRmapper: a fast and sensitive genome-hashing alignment tool.
Gontarz PM, Berger J, Wong CF.

Myblast 1.0.29 – Customized Biological Sequence Alignment tool

Myblast 1.0.29

:: DESCRIPTION

Myblast is the web-application of the customized biological sequence alignment tool.

::DEVELOPER

Lab of Systems and Network Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 Myblast

:: MORE INFORMATION