Pse-Analysis 1.0 – Sequence analysis based on Pseudo Components and Kernel methods

Pse-Analysis 1.0

:: DESCRIPTION

Pse-Analysis is a Python package for DNA/RNA and protein/peptide sequence analysis based on pseudo components and kernel methods.

::DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • Python

:: DOWNLOAD

Pse-Analysis

:: MORE INFORMATION

Citation

Liu B, Wu H, Zhang D, Wang X, Chou KC.
Pse-Analysis: a python package for DNA/RNA and protein/ peptide sequence analysis based on pseudo components and kernel methods.
Oncotarget. 2017 Feb 21;8(8):13338-13343. doi: 10.18632/oncotarget.14524. PMID: 28076851; PMCID: PMC5355101.

AAScan 2.2 / MutantChecker 1.3 / PCR Cloning 1.5 – Primer Design and Sequence Analysis for High-throughput Scanning Mutagenesis

AAScan 2.2 / MutantChecker 1.3 / PCR Cloning 1.5

:: DESCRIPTION

AAscan, PCRdesign and MutantChecker is a suite of programs for primer design and sequence analysis for high-throughput scanning mutagenesis.

AAScan (formely AlaScan) – batch primer design software for scanning mutagenesis
MutantChecker – helps to analyse the sequenceing results from scanning mutagenesis
PCR Cloning – design of primers for ligation-independent cloning

::DEVELOPER

Laboratory of Biomolecular Research (LBR)

:: SCREENSHOTS

aascan

MutantChecker

PCRCloning

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 AAScan, MutantCheckerPCR Cloning

:: MORE INFORMATION

Citation

PLoS One. 2013 Oct 30;8(10):e78878. doi: 10.1371/journal.pone.0078878. eCollection 2013.
AAscan, PCRdesign and MutantChecker: a suite of programs for primer design and sequence analysis for high-throughput scanning mutagenesis.
Sun D1, Ostermaier MK, Heydenreich FM, Mayer D, Jaussi R, Standfuss J, Veprintsev DB.

BW4SA – Burrows-Wheeler Transform for Sequence Analysis

BW4SA

:: DESCRIPTION

BW4SA is a generic, practical, versatile library for implementing a variety of (bio)sequence analysis algorithms in succinct space.

::DEVELOPER

GSA (Genome-scale algorithmics) group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 BW4SA

:: MORE INFORMATION

Citation

Djamal Belazzougui, Fabio Cunial, Juha Kärkkäinen, Veli Mäkinen
Versatile succinct representations of the bidirectional Burrows-Wheeler transform.
ESA 2013, Springer, Lecture Notes in Computer Science Volume 8125, 2013, pp 133-144

CAFE 1.0 – aCcelerated Alignment-FrEe sequence analysis

CAFE 1.0

:: DESCRIPTION

CAFE is a standalone software for efficient calculation of 28 alignment-free dissimilarity measures.

::DEVELOPER

Fengzhu Sun

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX

:: DOWNLOAD

CAFE

:: MORE INFORMATION

Citation

Lu YY, Tang K, Ren J, Fuhrman JA, Waterman MS, Sun F.
CAFE: aCcelerated Alignment-FrEe sequence analysis.
Nucleic Acids Res. 2017 Jul 3;45(W1):W554-W559. doi: 10.1093/nar/gkx351. PMID: 28472388; PMCID: PMC5793812.

CloVR 1.0 RC9 – Automated Sequence Analysis from Your Desktop

CloVR 1.0 RC9

:: 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.

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.

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.

OBITools 1.2.13 – Scripts and Library for Sequence Analysis

OBITools 1.2.13

:: 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.

TOUCAN 3.1.1 – Regulatory Sequence Analysis on Metazoan Genomes

TOUCAN 3.1.1

:: DESCRIPTION

TOUCAN is a workbench for regulatory sequence analysis on metazoan genomes : comparative genomics, detection of significant transcription factor binding sites, and detection of cis-regulatory modules (combinations of binding sites) in sets of coexpressed/coregulated genes.

::DEVELOPER

aertslab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • Java
:: DOWNLOAD

 TOUCAN

:: MORE INFORMATION

Citation

Stein Aerts, Peter Van Loo, Gert Thijs, Herbert Mayer, Rainer de Martin, Yves Moreau and Bart De Moor (2005)
TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis“.
Nucl Acids Res, vol. 33 (Web Server issue), W393-6.

SeqAn 2.4.0 – Open Source C++ Library of Sequences Analysis

SeqAn 2.4.0

:: 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.