CGAT Apps 0.4.0 – Scripts for Genomics and Next-generation Sequencing Analysis

CGAT Apps 0.4.0

:: DESCRIPTION

The CGAT App contains scripts and pipelines developed by CGAT. The collection contains scripts for genomics and next-generation sequencing analysis, but also general purpose scripts.

::DEVELOPER

Computational Genomics: Analysis and Training (GCAT)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • Python

:: DOWNLOAD

CGAT Apps

 :: MORE INFORMATION

Citation

Bioinformatics. 2014 May 1;30(9):1290-1. doi: 10.1093/bioinformatics/btt756. Epub 2014 Jan 5.
CGAT: computational genomics analysis toolkit.
Sims D1, Ilott NE, Sansom SN, Sudbery IM, Johnson JS, Fawcett KA, Berlanga-Taylor AJ, Luna-Valero S, Ponting CP, Heger A.

dali_sp – Script for DaliLite to perform Serial Structure Comparison

dali_sp

:: DESCRIPTION

dali_sp is a wrapper script for DaliLite to perform serial structure comparison and to merge output pairwise alignments into single multiple alignment.

::DEVELOPER

VU Institute of Biotechnology

:: SCREENSHOTS

N/A

::REQUIREMENTS

:: DOWNLOAD

 dali_sp

:: MORE INFORMATION

Omics Integrator 0.2 – Python Scripts for Analyzing Diverse Forms of ‘omic’ data

Omics Integrator 0.2

:: DESCRIPTION

Omics Integrator is package comprised of command-line tools designed to integrate high-throughput datasets such as gene expression, phospho-proteomic data and the results from genetic screens.

::DEVELOPER

The Fraenkel Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

  Omics Integrator

:: MORE INFORMATION

Citation

Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package.
Tuncbag N, Gosline SJ, Kedaigle A, Soltis AR, Gitter A, Fraenkel E.
PLoS Comput Biol. 2016 Apr 20;12(4):e1004879. doi: 10.1371/journal.pcbi.1004879

SeqToolBox 0.02 – A set of Perl modules and scripts for Operations on Sequence data

SeqToolBox 0.02

:: DESCRIPTION

SeqToolBox is a set of Perl modules and scripts for day to day operations on sequence data. Includes, parsers for standard file formats and some utility modules, such as modules for working with “sets”, a set of modules for handling NCBI taxonomy database etc. The bin directory contains some scripts to run jobs on clusters.

::DEVELOPER

Malay K Basu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

  SeqToolBox

:: MORE INFORMATION

PDBHighlight 1.1.0 – A RasMol Script database

PDBHighlight 1.1.0

:: DESCRIPTION

The aim of pdbHighlight is to maintain a searchable database of RasMol script files, designed to ‘highlight’ various features of the protein molecules whose structures are available in the Protein Data Bank

::DEVELOPER

Dan Bolser

 SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Perl

:: DOWNLOAD

 PDBHighlight

:: MORE INFORMATION

bioscripts.convert 0.4 – Biopython Scripts for Converting Molecular Sequences

bioscripts.convert 0.4

:: DESCRIPTION

bioscripts.convert provides scripts that use Biopython internally to simply convert multiple files on the commandline.

::DEVELOPER

Paul-Michael Agapow and Austin Burt (a.burt@imperial.ac.uk), Dept. Biology, University College London

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 bioscripts.convert

:: MORE INFORMATION

bloutminer 0.9.6 – Script for Mining data from BLAST Reports

bloutminer 0.9.6

:: DESCRIPTION

bloutminer is a script for mining data from BLAST reports. Allows you to specify e.g. an E-value cutoff, a length cutoff and a percent identity cutoff, and extract a list of the hits satisfying these cutoffs. I normally use an E-value cutoff of 10 for my BLAST searches, and then extracts hits with bloutminer, allowing me to change the cutoffs at a later stage without redoing the whole BLAST search. Is also able to “pool” sequences into groups, based on their sequence tags. In addition, it can also output the N number of best matches to a query.

::DEVELOPER

Johan Bengtsson

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX/ Windows
  • Perl

:: DOWNLOAD

  bloutminer

:: MORE INFORMATION

MS3toMimicS2 – MGF Conversion Script

MS3toMimicS2

:: DESCRIPTION

MS3toMimicS2 is a perl script to convert an MGF containing MS3 spectra to a MimicS2 MGF by replacing all precursor masses with the more accurate precursor masses from the survey scan.

::DEVELOPER

Steen Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows / MacOsX
  • Perl

:: DOWNLOAD

 MS3toMimicS2

:: MORE INFORMATION

Citation

Timm W, Ozlu N, Steen JJ, Steen H (2010)
The effect of high accuracy precursor masses on phosphopeptide identification from MS3 spectra Analytical Chemistry
Anal. Chem., 2010, 82 (10), pp 3977–3980 DOI: 10.1021/ac100118u

Proteomatic 1.2.1 – Platform for creating MS/MS data Analysis Workflows using Scripts

Proteomatic 1.2.1

:: DESCRIPTION

Proteomatic is a free data processing pipeline created for the purpose of evaluating mass spectrometric proteomics experiments. Functionality is provided via scripts, and these scripts can be chained together into a high-throughput data processing pipeline.

::DEVELOPER

Proteomatic team

:: SCREENSHOTS

Proteomatic

:: REQUIREMENTS

  • Windows/ MacOsX / Linux

:: DOWNLOAD

 Proteomatic

:: MORE INFORMATION

Citation

Proteomics to go: Proteomatic enables the user-friendly creation of versatile MS/MS data evaluation workflows
Specht M., Kuhlgert S., Fufezan C., Hippler M.
Bioinformatics (2011) 27(8): 1183-1184, doi: 10.1093/bioinformatics/btr081

modplus – script for Modeller to perform Sequence-structure Alignment

modplus

:: DESCRIPTION

modplus is a wrapper script for Modeller; it performs sequence-structure alignment and preprocessing steps to model target sequence. The input to the program is a multiple alignment of target and template sequences in the FASTA format. The template structures will be supposed to be accessible in a given location.

::DEVELOPER

Laboratory of Bioinformatics, VU Institute of Biotechnology

:: SCREENSHOTS

N/A

::REQUIREMENTS

:: DOWNLOAD

 modplus

:: MORE INFORMATION