Tag: CAST

CAST 1.0 – Compositional Bias Detection Algorithm

CAST 1.0

:: DESCRIPTION

CAST is a novel algorithm for low-complexity region detection and selective masking. The algorithm is based on multiple-pass Smith-Waterman comparison of the query sequence against twenty homopolymers with infinite gap penalties. The output of the algorithm is both the masked query sequence for further analysis, e.g. database searches, as well as the regions of low complexity.

::DEVELOPER

Biophysics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Vasilis J. Promponas, Anton J. Enright, Sophia Tsoka, David P. Kreil, Christophe Leroy,Stavros J. Hamodrakas, Chris Sander, and Christos A. Ouzounis
CAST: an iterative algorithm for the complexity analysis of sequence tracts
Bioinformatics (2000), 16(10), 915-922.

CAST 1.2.2 – Compression-accelerated BLAST and BLAT

CAST 1.2.2

:: DESCRIPTION

CAST is a set of tools that compress data in a way that allows direct computation on the compressed data. Compression-accelerated BLAST (CaBLAST) and Compression-accelerated BLAT (CaBLAT) are two prototype implementations of alignment and sequence search algorithms that apply “compressive genomics” : i.e., they exploit redundancy in genomic data sets by compressing data in a way that allows direct computation on the compressed data.

::DEVELOPER

Berger Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX
  • C++ Compiler
  • NCBI C++ Toolkit
  • BLAST+
  • BLAT

:: DOWNLOAD

  CAST

:: MORE INFORMATION

Citation:

Nat Biotechnol. 2012 Jul 10;30(7):627-30. doi: 10.1038/nbt.2241.
Compressive genomics.
Loh PR, Baym M, Berger B.