Tag: CAPS

CAPS 2.0 – Coevolution Analysis using Protein Sequences

CAPS 2.0

:: DESCRIPTION

CAPS (Coevolution Analysis using Protein Sequences) is a PERL based software that identifies co-evolution between amino acid sites. Blosum-corrected amino acid distances are used to identify amino acid co-variation. The phylogenetic sequence relationships are used to remove the phylogenetic and stochastic dependencies between sites. The 3D protein structure is used to identify the nature of the dependencies between co-evolving amino acid sites.

CAPS Online Version

::DEVELOPER

Dr Mario Fares 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Perl

:: DOWNLOAD

 CAPS

:: MORE INFORMATION

Citation

CAPS: coevolution analysis using protein sequences.
Fares MA, McNally D.
Bioinformatics. 2006 Nov 15;22(22):2821-2. Epub 2006 Sep 27.

SNP2CAPS – SNP and INDEL Analysis Tool for CAPS Marker Development

SNP2CAPS

:: DESCRIPTION

SNP2CAPS facilitates the computational conversion of SNPs into CAPS markers. A simple algorithm involves the screening of multiply-aligned sequences for restriction sites followed by a selection pipeline that allows the deduction of CAPS candidates by the identification of putative alternative restriction sites.

::DEVELOPER

Thomas Thiel  at the IPK-Gatersleben

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux/  MacOSX
  • Perl

:: DOWNLOAD

 SNP2CAPS

:: MORE INFORMATION

Citation

T. Thiel, R. Kota, I. Grosse, N. Stein, and A. Graner.
SNP2CAPS: a SNP and INDEL analysis tool for CAPS marker development.
Nucleic Acids Research, 32(1):e5, 2004.