GASSST 1.28 – Global Alignment Short Sequence Search Tool

GASSST 1.28

:: DESCRIPTION

GASSST (Global Alignment Short Sequence Search Tool) is 2-fold—achieving high performance with no restrictions on the number of indels with a design that is still effective on long reads.

::DEVELOPER

Dominique Lavenier , Guillaume Rizk , Damien Fleury

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
GNU gcc compiler

:: DOWNLOAD

GASSST

:: MORE INFORMATION

Citation

Guillaume Rizk and Dominique Lavenier
GASSST: global alignment short sequence search tool
Bioinformatics (2010) 26 (20): 2534-2540.

MetaDomain 20140716 – HMM-based Protein Domain Classification tool for Short Sequence

MetaDomain 20140716

:: DESCRIPTION

MetaDomain can accurately align short reads generated by new sequencing technologies to to protein domains and annotate domain expression level.

::DEVELOPER

Dr. Yanni Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
G++

:: DOWNLOAD

MetaDomain

:: MORE INFORMATION

Citation

Pac Symp Biocomput. 2012:271-82.
Metadomain: a profile HMM-based protein domain classification tool for short sequences.
Zhang Y, Sun Y.

SeqMap 1.0.13 – Map Millions of Short Sequences to Genome

SeqMap 1.0.13

:: DESCRIPTION

SeqMap is a tool for mapping large amount of oligonucleotide to the genome. It is designed for finding all the places in a genome where an oligonucleotide could potentially come from. SeqMap can efficiently map as many as dozens of millions of short sequences to a genome of several billions of nucleotides. While doing the mapping, several mutations as well as insertions/deletions of the nucleotide bases in the sequences can be tolerated and furthermore detected. Various input and output formats are supported, as well as many command line options for tuning almost every steps in the mapping process.

::DEVELOPER

Hui Jiang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX / Windows

:: DOWNLOAD

SeqMap

:: MORE INFORMATION

Citation

Jiang, H., Wong, W.H. (2008)
SeqMap: Mapping Massive Amount of Oligonucleotides to the Genome,
Bioinformatics, 24 (20): 2395-2396.

SSEdit 6.08 – Single (Short) Sequence Editor

SSEdit 6.08

:: DESCRIPTION

SSEdit is a MacOS X application for viewing and editing single sequences. Input and output files in FASTA, NRBF, Staden and other formats are supported with the capability to recognise some by the file extension name.

::DEVELOPER

Department of Biochemistry, University of Otago

:: SCREENSHOTS

N/A

:: REQUIREMENTS

MacOsX

:: DOWNLOAD

SSEdit

:: MORE INFORMATION

SR-ASM – DNA Assembly of the Short Sequences coming from 454 sequencer

SR-ASM

:: DESCRIPTION

SR-ASM (Short Reads ASseMbly) algorithm is designed for DNA assembly of the short sequences coming from 454 sequencers.

::DEVELOPER

The Bioinformatics Group, Poznan University of Technology.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

SR-ASM

:: MORE INFORMATION

Citation

Comput Biol Chem. 2009 Jun;33(3):224-30. Epub 2009 May 3.
Whole genome assembly from 454 sequencing output via modified DNA graph concept.
Blazewicz J, Bryja M, Figlerowicz M, Gawron P, Kasprzak M, Kirton E, Platt D, Przybytek J, Swiercz A, Szajkowski L.

PatMaN 1.2.2 – DNA Pattern Matcher for Short Sequences

PatMaN 1.2.2

:: DESCRIPTION

Patman searches for short patterns in large DNA databases, allowing for approximate matches. It is optimized for searching for many small pattern at the same time, for example microarray probes.

::DEVELOPER

Department of Genetics/Bioinformatics – Max Planck Institut

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

Patman

:: MORE INFORMATION

Citation

Kay Prüfer et al.
PatMaN: rapid alignment of short sequences to large databases.
Bioinformatics. 2008 Jul 1;24(13):1530-1