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.

BlatView – Mapping EST’s to Genomes

BlatView

:: DESCRIPTION

BlatView maps results from a BLAT search on to the corresponding genome/chromosome/BAC clones.

::DEVELOPER

BlatView team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java

:: DOWNLOAD

 BlatView

:: MORE INFORMATION

References:

Kent W.J. (2002)
BLAT–the BLAST-like alignment tool.
Genome Res. 12(4):656-64.

BLAT 36 – Rapid mRNA/DNA & Cross-species Protein Alignments

BLAT 36

:: DESCRIPTION

BLAT (BLAST -like alignment tool) is a bioinformatics software a tool which performs rapid mRNA/DNA and cross-species protein alignments. BLAT is more accurate and 500 times faster than popular existing tools for mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing vertebrate sequences.

BLAT Online Version

::DEVELOPER

Jim Kent

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX

:: DOWNLOAD

 BLAT ; Source Code

:: MORE INFORMATION

Citation

Kent, W.J. 2002.
BLAT — The BLAST-Like Alignment Tool.
Genome Research 4: 656-664

SCUBAT – Scaffolding Contigs using BLAT and Transcripts

SCUBAT

:: DESCRIPTION

SCUBAT is a perl script uses any set of transcripts to identify cases where a transcript is split over multiple genome fragments and attempts to use this information to scaffold the genome.

::DEVELOPER

The Blaxter Lab at The Institute of Evolutionary Biology University of Edinburgh

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • BLAT
  • CAP3
  • Perl

:: DOWNLOAD

 SCUBAT

:: MORE INFORMATION