ITEP 1.1 – Integrated Toolkit for Exploration of Pan-genomes

ITEP 1.1

:: DESCRIPTION

ITEP is a suite of scripts and Python libraries for the comparison of microbial genomes. It includes tools for de novo protein family prediction by clustering, ortholog detection, analysis of functional domains, identification of core and variable genes and gene regions, sequence alignments and tree generation, cluster curation, and the integration of cross-genome analysis and metabolic networks for study of metabolic network evolution.

::DEVELOPER

The Hood-Price Lab for Systems Biomedicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/ MacOsX
  • Python

:: DOWNLOAD

 ITEP

:: MORE INFORMATION

Citation

BMC Genomics. 2014 Jan 3;15:8. doi: 10.1186/1471-2164-15-8.
ITEP: an integrated toolkit for exploration of microbial pan-genomes.
Benedict MN, Henriksen JR, Metcalf WW, Whitaker RJ, Price ND1.

CRAVAT 4.0 – Cancer-related Analysis of Variants Toolkit

CRAVAT 4.0

:: DESCRIPTION

CRAVAT is a web server with simple interface where cancer-related analysis of variants are performed.CRAVAT currently employs three analysis tools, CHASM, SNVGet, and VEST.

::DEVELOPER

Karchin Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

CRAVAT: cancer-related analysis of variants toolkit.
Douville C, Carter H, Kim R, Niknafs N, Diekhans M, Stenson PD, Cooper DN, Ryan M, Karchin R.
Bioinformatics. 2013 Mar 1;29(5):647-8. doi: 10.1093/bioinformatics/btt017. Epub 2013 Jan 16.

DistMap 1.0 – A Toolkit for Distributed Short Read Mapping on a Hadoop Cluster

DistMap 1.0

:: DESCRIPTION

DistMap is a user-friendly pipeline designed to map short reads in a MapReduce framework on a local Hadoop cluster.

DEVELOPER

Institute of Population Genetics, University of Veterinary Medicine Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Java
  • Perl
  • Mapper executable
  •  MergeSamFiles.jar and SortSam.jar from PICARD (http://picard.sourceforge.net).
  • A working Hadoop cluster.

:: DOWNLOAD

 DistMap

:: MORE INFORMATION

Citation:

Pandey RV, Schlötterer C. (2013)
DistMap: a toolkit for distributed short read mapping on a Hadoop cluster.
PLoS One. 8(8):e72614.

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.

BAMTOOLS 2.4.0 – C++ API and Toolkit for Analyzing and Managing BAM files

BAMTOOLS 2.4.0

:: DESCRIPTION

BamTools provides both a programmer’s API and an end-user’s toolkit for handling BAM files.

::DEVELOPER

The MarthLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 BAMTOOLS

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jun 15;27(12):1691-2. Epub 2011 Apr 14.
BamTools: a C++ API and toolkit for analyzing and managing BAM files.
Barnett DW, Garrison EK, Quinlan AR, , Strömberg MP, Marth GT.

VEGA ZZ 3.0.5.12 – Molecular Modeling Toolkit

VEGA ZZ 3.0.5.12

:: DESCRIPTION

VEGA ZZ is the evolution of the well known VEGA OpenGL package and includes several new features and enhancements making your research jobs very easy. VEGA was originally developed to create a bridge between most of the molecular software packages only, but in the years, enhancing its features, it’s evolved to a complete molecular modelling suite. This software is FREE for non-profit academic uses.

::DEVELOPER

Drug Design Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 VEGA ZZ

:: MORE INFORMATION

Citation

Pedretti A., Villa L., Vistoli G.,
VEGA – An open platform to develop chemo-bio-informatics applications, using plug-in architecture and script” programming“,
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, Vol. 18, 167-173 (2004).

BATS – A Basic Analysis Toolkit for Biological Sequences

BATS

:: DESCRIPTION

BATS consists of a collection of libraries that can be used to run basic sequence analysis tasks. Routines for global alignment (LCS from Fragments, Edit Distance with Gaps), local alignment (approximata string matching with K mismateches or differences), and statistical analysis (Filter, Z-Score and Model Generation ) are included.

::DEVELOPER

Raffaele Giancarlo

:: SCREENSHOTS

BATS2

:: REQUIREMENTS

  • Linux / MacOSX / Windows
  • Perl

:: DOWNLOAD

 BATS

:: MORE INFORMATION

Citation

Algorithms Mol Biol. 2007 Sep 18;2:10.
A basic analysis toolkit for biological sequences.
Giancarlo R1, Siragusa A, Siragusa E, Utro F.

DynaMIT 1.0.4 – Dynamic Motif Integration Toolkit

DynaMIT 1.0.4

:: DESCRIPTION

DynaMIT is a flexible platform for sequence and structure motifs integration, providing the means to execute multiple motif search tools, integrate their output and display the obtained results in a plethora of different ways.

::DEVELOPER

Laboratory of Translational Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • Python

:: DOWNLOAD

 DynaMIT

:: MORE INFORMATION

Citation

DynaMIT: the dynamic motif integration toolkit.
Dassi E, Quattrone A.
Nucleic Acids Res. 2015 Aug 7. pii: gkv807

RAmiRNA – Viral mature MicroRNA prediction Toolkit

RAmiRNA

:: DESCRIPTION

RAmiRNA (RAdicalmiRNA detector) is a software to solve the problem of custom development of prediction models for mature miRNAs using support vector machine (SVM) learning.

::DEVELOPER

Indo-Russian Centre for Biotechnology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RAmiRNA

:: MORE INFORMATION

Citation

Bioinformation. 2012;8(12):581-5. doi: 10.6026/97320630008581. Epub 2012 Jun 28.
RAmiRNA: Software suite for generation of SVMbased prediction models of mature miRNAs.
Tyagi V, Prasad CS.

bPE toolkit – Basic Protein Engineering Toolkit

bPE toolkit

:: DESCRIPTION

bPE toolkit consists of 5 independent programs, that can be incorporated in a pipeline of various protein structure files. The programs include tools for chirality check for amino acids (ProChiral), contact map generation (CoMa), data redundancy (DaRe), hydrogen bond potential energy (HyPE) and electrostatic interaction energy (EsInE).

::DEVELOPER

bPE toolkit team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 bPE toolkit

:: MORE INFORMATION

Citation

bPE toolkit: toolkit for computational protein engineering.
Jerath G, Hazam PK, Ramakrishnan V.
Syst Synth Biol. 2014 Dec;8(4):337-41. doi: 10.1007/s11693-014-9156-4.