SeAMotE – Sequence Analysis of Motifs Enrichment

SeAMotE

:: DESCRIPTION

SeAMotE allows fast and accurate large-scale de novo motif discovery in nucleic acid sequences.

::DEVELOPER

Tartaglia Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Genomics. 2014 Oct 23;15:925. doi: 10.1186/1471-2164-15-925.
SeAMotE: a method for high-throughput motif discovery in nucleic acid sequences.
Agostini F, Cirillo D, Ponti RD, Tartaglia GG1.

SAPTF 1.7 – Sequence Analysis Plugin Tool Framework

SAPTF 1.7

:: DESCRIPTION

SAPTF (Sequence Analysis Plugin Tools Framework) is designed as a very simple way to provide sequence analysis tools on the web. It saves all the effort of creating the actual pages and CGI scripts – all that is needed is the tool itself (which can return HTML or just plain text) and a simple XML configuration file. SAPTF will even deal with very slow long-running programs (like BLAST or ClustalW) which might make the user wonder whether anything is happening, or may need some sort of wait-page to stop the web server from timing out – SAPTF deals with this through AJAX.

::DEVELOPER

Andrew C.R. Martin’s Bioinformatics Group at UCL

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SAPTF

:: MORE INFORMATION

DNAMAN 10.0 – Integrated System for Sequence Analysis

DNAMAN 10.0

:: DESCRIPTION

DNAMAN is a one-for-all software package for molecular biology applications. This package provides an integrated system with versatile functions for high efficiency sequence analysis. You no longer need one program for restriction analyses and others for multiple sequence alignment, designing PCR primers, protein sequence analysis or drawing plasmids…

::DEVELOPER

Lynnon Corporation

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX

:: DOWNLOAD

 DNAMAN

:: MORE INFORMATION

SeqAn 2.2.0 – Open Source C++ Library of Sequences Analysis

SeqAn 2.2.0

:: DESCRIPTION

SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. Our library applies a unique generic design that guarantees high performance, generality, extensibility, and integration with other libraries. SeqAn is easy to use and simplifies the development of new software tools with a minimal loss of performance.

::DEVELOPER

SeqAn Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • C++ Compiler

:: DOWNLOAD

 SeqAn

:: MORE INFORMATION

Citation

SeqAn an efficient, generic C++ library for sequence analysis.
Döring A, Weese D, Rausch T, Reinert K.
BMC Bioinformatics. 2008 Jan 9;9:11.

OBITools 1.2.6 – Scripts and Library for Sequence Analysis

OBITools 1.2.6

:: DESCRIPTION

OBITools is a set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding.

::DEVELOPER

OBITools team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/windows/MacOsX
  • Python

:: DOWNLOAD

 OBITools

:: MORE INFORMATION

Citation

OBITools: a Unix-inspired software package for DNA metabarcoding.
Boyer F, Mercier C, Bonin A, Le Bras Y, Taberlet P, Coissac E.
Mol Ecol Resour. 2015 May 9. doi: 10.1111/1755-0998.12428.

MoSDi 1.3 – Sequence Analysis Toolkit for Bioinformatics

MoSDi 1.3

:: DESCRIPTION

MoSDi (Motif Statistics and Discovery) contains a lot of sequence analysis algorithms, including methods for

  • motif statistics, e.g. compute the exact occurrence count distribution of a motif,
  • exact motif discovery: extraction of motifs with provably optimal p-value,
  • analysis of pattern matching algorithms: compute (for given algorithm and pattern) the exact distribution of the number of character accesses caused by searching a random text,
  • statistics of fragment masses resulting from proteolytic cleavage of proteins,
  • computing the expectated read length of sequencing reads for a given dispensation order (for 454 or IonTorrent),
  • analysing sensitivity of spaced alignment seeds.

::DEVELOPER

Tobias Marschall

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java 

:: DOWNLOAD

 MoSDi

:: MORE INFORMATION

Citation

IEEE/ACM Trans Comput Biol Bioinform. 2012 Nov-Dec;9(6):1737-50.
Probabilistic arithmetic automata and their applications.
Marschall T, Herms I, Kaltenbach HM, Rahmann S.

GATA 0.7 – Graphic Alignment Tool for Comparative Sequence Analysis

GATA 0.7

:: DESCRIPTION

GATA is a stand alone, platform independent, graphic alignment tool for comparative sequence analysis. It makese use of BLAST to graphically align two DNA sequences creating box-line-box representations of window scored local alignments. Gata can also display extensive gene annotation using a standardized GFF format.

::DEVELOPER

Eisen Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

 GATA

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2005 Jan 17;6:9.
GATA: a graphic alignment tool for comparative sequence analysis.
Nix DA, Eisen MB.

CloVR 1.0 RC7 – Automated Sequence Analysis from Your Desktop

CloVR 1.0 RC7

:: DESCRIPTION

CloVR is a desktop application that integrates state-of-the-art genomic tools in a robust, user friendly, and fully automated software package with optional support for cloud computing platforms. CloVR currently bundles push-button pipelines for microbial genomics, including single-genome projects, 16S rRNA sequence analysis, and metagenomic sequencing projects. Additional pipelines for comparative genome analysis, prokaryotic and eukaryotic RNA-sequencing and viral genomics are planned.

::DEVELOPER

Institute for Genome SciencesUniversity of Maryland School of Medicine

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 CloVR

:: MORE INFORMATION

Citation:

Angiuoli SV, Matalka M, Gussman G, Galens K, Vangala M, Riley DR, Arze C, White JR, White O and Fricke WF.
CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing.
BMC Bioinformatics. 2011 Aug;12:356.

Vector NTI Advance 11.5.4 – Sequence Analysis and Data Management software

Vector NTI Advance 11.5.4

:: DESCRIPTION

Vector NTI® Advance software is the most highly integrated, multifunctional desktop sequence analysis application suite available today and provides superior integration, data management, and scalability.

::DEVELOPER

Life Technologies

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OS X with Parallels

:: DOWNLOAD

Vector NTI Advance

:: MORE INFORMATION