Chromas 2.6 / ChromasPro 2.0.1 – Sequence & Chromatogram Editor

Chromas 2.6 / ChromasPro 2.0.1

:: DESCRIPTION

Chromas is a low-cost chromatogram file editor with search, vector sequence detection and multi-format sequence export functions, plus powerful batch processing.

ChromasPro is a low-cost sequence and chromatogram editor with search, vector sequence detection, contiguous sequence assembly and restriction and open-reading-frame mapping.

::DEVELOPER

Technelysium Pty Ltd

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

Chromas ,  ChromasPro

:: MORE INFORMATION

DNA Baser 4.36 – DNA Sequence Assembly & Analysis

DNA Baser 4.36

:: DESCRIPTION

DNA Baser is a tool for DNA sequence assembly, DNA sequence analysis, contig editing, and mutation detection. It also offers a powerful chromatogram viewer/editor.

::DEVELOPER

Heracle BioSoft

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

DNA Baser

:: MORE INFORMATION

MEME 4.11.2 – Discovering Motifs within the Sequences

MEME 4.11.2

:: DESCRIPTION

MEME (Multiple Em for Motiv Elicitation) is a tool for discovering motifs in a group of related DNA or protein sequences.A motif is a sequence pattern that occurs repeatedly in a group of related protein or DNA sequences. MEME represents motifs as position-dependent letter-probability matrices which describe the probability of each possible letter at each position in the pattern. Individual MEME motifs do not contain gaps. Patterns with variable-length gaps are split by MEME into two or more separate motifs.MEME takes as input a group of DNA or protein sequences and outputs as many motifs as requested. MEME uses statistical modeling techniques to automatically choose the best width, number of occurrences, and description for each motif.

MCAST searches sequences for clusters of matches to one or more nucleotide motifs

::DEVELOPER

MEME Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  MEME

:: MORE INFORMATION

Citation

MCAST: Scanning for cis-regulatory motif clusters.
Grant CE, Johnson J, Bailey TL, Noble WS.
Bioinformatics. 2015 Dec 24. pii: btv750

The MEME Suite.
Bailey TL, Johnson J, Grant CE, Noble WS.
Nucleic Acids Res. 2015 May 7. pii: gkv416.

Timothy L. Bailey, Mikael Bodén, Fabian A. Buske, Martin Frith, Charles E. Grant, Luca Clementi, Jingyuan Ren, Wilfred W. Li, William S. Noble,
MEME SUITE: tools for motif discovery and searching“,
Nucleic Acids Research, 37:W202-W208, 2009

Circoletto 20151219 – Visualize Sequence Similarity with Circos

Circoletto 20151219

:: DESCRIPTION

Circoletto is a rather beautiful way to visualise sequence similarity from BLAST results (which you can either create through Circoletto, or upload your own).

::DEVELOPER

The Bioinformatics Analysis Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • BLAST
  • Circos

:: DOWNLOAD

 Circoletto

:: MORE INFORMATION

Citation:

Bioinformatics. 2010 Oct 15;26(20):2620-1. Epub 2010 Aug 24.
Circoletto: visualizing sequence similarity with Circos.
Darzentas N.

Change-O 0.3.2 – Analyzing Immunoglobulin Sequences

Change-O 0.3.2

:: DESCRIPTION

Change-O is a collection of tools for analyzing immunoglobulin sequences.

::DEVELOPER

the Kleinstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

 Change-O

:: MORE INFORMATION

Citation

Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data.
Gupta NT, Vander Heiden J, Uduman M, Gadala-Maria D, Yaari G, Kleinstein SH.
Bioinformatics. 2015 Jun 10. pii: btv359.

JAR3D – Predicting RNA 3D Motifs in Sequences

JAR3D

:: DESCRIPTION

JAR3D scores RNA hairpin and internal loop sequences against motif groups from the RNA 3D Motif Atlas, by exact sequence match for sequences already observed in 3D and by probabilistic scoring and edit distance for novel sequences.

::DEVELOPER

BGSU RNA Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

JAR3D Webserver: Scoring and aligning RNA loop sequences to known 3D motifs.
Roll J, Zirbel CL, Sweeney B, Petrov AI, Leontis N.
Nucleic Acids Res. 2016 May 27. pii: gkw453

Identifying novel sequence variants of RNA 3D motifs,
Craig L. Zirbel, James Roll, Blake A. Sweeney, Anton I. Petrov, Meg Pirrung, and Neocles Leontis.
Nucleic Acids Res. 2015 Sep 3;43(15):7504-20. doi: 10.1093/nar/gkv651

Kraken 0.10.5-beta – Kraken Taxonomic Sequence Classification System

Kraken 0.10.5-beta

:: DESCRIPTION

Kraken is a very fast system for taxonomic classification of short or long DNA sequences from a microbiome or metagenomic sample.

::DEVELOPER

The Center for Computational Biology at Johns Hopkins University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

 Kraken

:: MORE INFORMATION

Citation

Genome Biol. 2014 Mar 3;15(3):R46. doi: 10.1186/gb-2014-15-3-r46.
Kraken: ultrafast metagenomic sequence classification using exact alignments.
Wood DE, Salzberg SL.

RENT 0.1/ RentPlus 0.1- Inferring Local Trees with Recombinant Population Sequences

RENT 0.1/ RentPlus 0.1

:: DESCRIPTION

RENT is a program for inferring local tree topologies from recombinant SNP haplotypes.

RentPlus is a tool for reconstructing local tree topologies for a set of population SNP haplotypes undergoing recombination.

::DEVELOPER

Yufeng Wu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 RENT , RentPlus

:: MORE INFORMATION

Citation:

IEEE/ACM Trans Comput Biol Bioinform. 2011 Jan-Mar;8(1):182-93. doi: 10.1109/TCBB.2009.27.
New methods for inference of local tree topologies with recombinant SNP sequences in populations.
Wu Y.

MochiView 1.46 – Genomic Sequences Browser

MochiView 1.46

:: DESCRIPTION

MochiView is Java software that integrates browsing of genomic sequences, features, and data with DNA motif visualization and analysis

::DEVELOPER

the Johnson Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX /  Linux
  • Java

:: DOWNLOAD

 MochiView

:: MORE INFORMATION

Citation

Oliver R Homann and Alexander D Johnson
MochiView: versatile software for genome browsing and DNA motif analysis
BMC Biology 2010, 8:49

Paraclu 9 – Find Clusters in Data attached to Sequences

Paraclu 9

:: DESCRIPTION

Paraclu finds clusters in data attached to sequences. It was first applied to transcription start counts in genome sequences, but it could be applied to other things too. Paraclu is intended to explore the data, imposing minimal prior assumptions, and letting the data speak for itself.

::DEVELOPER

Computational Biology Research Center[CBRC]

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ compiler

:: DOWNLOAD

 Paraclu

:: MORE INFORMATION

Citation

MC Frith, E Valen, A Krogh, Y Hayashizaki, P Carninci, A Sandelin,
A code for transcription initiation in mammalian genomes,
Genome Research 2008 18(1):1-12.