Tag: Cross-species

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.

CSGM Designer – Cross Species Genic Marker Designer

CSGM Designer

:: DESCRIPTION

CSGM Designer has been developed with purposes of facilitating easy and systematic design of cross-species genic markers.

::DEVELOPER

CSGM Designer team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

CSGM Designer: a platform for designing cross-species intron-spanning genic markers linked with genome information of legumes.
Kim JH, Lee C, Hyung D, Jo YJ, Park JS, Cook DR, Choi HK.
Plant Methods. 2015 Apr 18;11:30. doi: 10.1186/s13007-015-0074-6.

Heinz 2.0 / xHeinz 1.2 – Single / Cross-species Module Discovery

Heinz 2.0 /xHeinz 1.2

:: DESCRIPTION

Heinz is a tool for single-species active module discovery.

xHeinz is a software solver that searches for active subnetwork modules that are conserved between two species. It uses a branch-and-cut algorithm that finds provably optimal or near-optimal solutions.

::DEVELOPER

Algorithmic Bioinformatics, Heinrich-Heine-Universität Düsseldorf

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

Heinz / xHeinz

:: MORE INFORMATION

Citation

xHeinz: An algorithm for mining cross-species network modules under a flexible conservation model.
El-Kebir M, Soueidan H, Hume T, Beisser D, Dittrich M, Müller T, Blin G, Heringa J, Nikolski M, Wessels LF, Klau GW.
Bioinformatics. 2015 May 27. pii: btv316

PhosphOrtholog – Cross-species Mapping of Orthologous Protein Post-translational Modification

PhosphOrtholog

:: DESCRIPTION

PhosphOrtholog is a tool to map post-translational modification sites on proteins orthologous across species

::DEVELOPER

PhosphOrtholog team

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web server

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PhosphOrtholog: a web-based tool for cross-species mapping of orthologous protein post-translational modifications.
Chaudhuri R, Sadrieh A, Hoffman NJ, Parker BL, Humphrey SJ, St?ckli J, Hill AP, James DE, Yang JY.
BMC Genomics. 2015 Aug 19;16(1):617. doi: 10.1186/s12864-015-1820-x.

SCSC – Cross-species Soft Clustering

 

SCSC

:: DESCRIPTION

SCSC (Soft Cross Species Clustering) clustering two species gene expression data, and identifies shared as well as species-specific co-expression modules.

::DEVELOPER

Zhong Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

SCSC

:: MORE INFORMATION

Citation

PLoS Comput Biol. 2010 Mar 12;6(3):e1000707. doi: 10.1371/journal.pcbi.1000707.
Modeling co-expression across species for complex traits: insights to the difference of human and mouse embryonic stem cells.
Cai J, Xie D, Fan Z, Chipperfield H, Marden J, Wong WH, Zhong S.