Mosaic 1.05 – a visual framework for Sequence Analysis using N-grams and Spectral rearrangement

Mosaic 1.05

:: DESCRIPTION

Mosaic is a software application to visually analyze sequence relationships. The similarities between the sequences of a given set are displayed within a matrix (mosaic plot), which enables the visual identification of clusters of related sequences, outliers or other sequences with special properties.

::DEVELOPER

Mosaic team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python
  • matplotlib

:: DOWNLOAD

  Mosaic

:: MORE INFORMATION

Citation

Stefan R. Maetschke, Karin S. Kassahn, Jasmyn A. Dunn, Siew P. Han, Eva Z. Curley, Katryn J. Stacey, Mark A. Ragan
A visual framework for sequence analysis using n-grams and spectral rearrangement
Bioinformatics. 2010 Mar 15;26(6):737-44. doi: 10.1093/bioinformatics/btq042

PSAAM – Protein Sequence Analysis And Modelling

PSAAM

:: DESCRIPTION

PSAAM (Protein Sequence Analysis And Modelling) includes many useful features for analysis of structural information from sequence data, cartoons for graphical representation of secondary structures, prediction programs, and prediction aids, a ribosome function for generation of coordinates sets in PDB format (including Header information) for viewing by molecular graphics packages (examples, see also PDVWIN), and a SeqPlot function for plotting secondary structural models (helical cylinders and wheels, coils, etc., with each residue indicated by a circle, color-coded (or coded by line thickness) according to the current physico-chemical index.

::DEVELOPER

A.R. CROFTS

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

PSAAM

:: MORE INFORMATION

Mussa 1.1.1 – Multi-Species Sequence Analysis

Mussa 1.1.1

:: DESCRIPTION

Mussa (Multi-Species Sequence Analysis) is a bioinformatics tool for finding and visualizing regions of conserved DNA by comparing across several species. It has been found that conserved regions are frequently enriched for regions that are functionally important. Thus Mussa is a tool to help discover previously unknown functional DNA elements.

::DEVELOPER

Mussa Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/MacOsx/WIndows

:: DOWNLOAD

 Mussa

:: MORE INFORMATION

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

:: 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.