ReAlignerV 8.1.4 – Genomic Alignment Tool & Implementation

ReAlignerV 8.1.4

:: DESCRIPTION

ReAlignerV is an alignment tool focusing on genomic nucleotide sequences upstream of genes.

::DEVELOPER

Hisakazu IWAMA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Perl

:: DOWNLOAD

 ReAlignerV

:: MORE INFORMATION

Citation:

Iwama H. et al.
ReAlignerV: Web-based genomic alignment tool with high specificity and robustness estimated by species-specific insertion sequences
BMC Bioinformatics. 9(1):112,

Iwama H & Gojobori T,
Highly conserved upstream sequences for transcription factor genes and implications for the regulatory network.
PNAS 2004, 101(49):17156-17161.

LAGAN 2.0 – Genomic Alignment

LAGAN 2.0

:: DESCRIPTION

Lagan Tookit are tools for genomic alignment. These include the MLAGAN multiple alignment tool, and Shuffle-LAGAN for alignment with rearrangements.. All three are based on the CHAOS local alignment tool and combine speed (regions up to several megabases can be aligned in minutes) with high accuracy.

::DEVELOPER

LAGAN team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 LAGAN

:: MORE INFORMATION

Citation

Michael Brudno, Chuong Do, Gregory Cooper, Michael F. Kim, Eugene Davydov, Eric D. Green, Arend Sidow and Serafim Batzoglou
LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA,
Genome Research 2003 Apr;13(4):721-31.

Michael Brudno, Sanket Malde, Alexander Poliakov, Chuong Do, Olivier Courone, Inna Dubchak, and Serafim Batzoglou
Glocal alignment: finding rearrangements during alignment.
Bioinformatics. 2003;19 Suppl 1:i54-62.

Michael Brudno, Michael Chapman, Berthold Gottgens, Serafim Batzoglou, and Burkhard Morgenstern
Fast and sensitive multiple alignment of large genomic sequences
BMC Bioinformatics, 4:66 2003.