ArchTEx 1.0.6 – Accurate Extraction and Visualization of Next-Generation Sequence data

ArchTEx 1.0.6

:: DESCRIPTION

ArchTEx (Architectural Tag Extender) identifies the optimal extension of sequence tags based on the maximum correlation between forward and reverse tags and extracts and visualizes sites of interest using the predicted extension.

::DEVELOPER

Buck Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows
  • JRE

:: DOWNLOAD

 ArchTEx

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Apr 1;28(7):1021-3. doi: 10.1093/bioinformatics/bts063. Epub 2012 Feb 2.
ArchTEx: accurate extraction and visualization of next-generation sequence data.
Lai WK1, Bard JE, Buck MJ.

GFF-Ex 2.3 – Genome Feature Extraction package

GFF-Ex 2.3

:: DESCRIPTION

GFF-Ex, a Genome Feature extraction package extracts Gene, Exon, Intron, Upstream Region of Gene (Promoters), Intergenic and CDS/cDNA sequences by just tweeting in the Genome Feature File (gff) along with the corresponding genome/chromosome sequence.

::DEVELOPER

Bioinformatics Centre ICGEB New Delhi

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 GFF-Ex

:: MORE INFORMATION

Citation

BMC Res Notes. 2014 May 24;7:315. doi: 10.1186/1756-0500-7-315.
GFF-Ex: a genome feature extraction package.
Rastogi A, Gupta D

MassSpec 1.1 – Peak list Extraction from Proteomic Mass Spectra

MassSpec 1.1

:: DESCRIPTION

MassSpecis a MATLAB implementation of the peak list extraction procedure

::DEVELOPER

laboratorio di Bioinformatica e Biologia Sintetica – Univ. of Pavia

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • Matlab

:: DOWNLOAD

 MassSpec

:: MORE INFORMATION

Citation

BMC Bioinformatics 2010, 11:518 doi:10.1186/1471-2105-11-518
Accurate peak list extraction from proteomic mass spectra for identification and profiling studies.
Barbarini N, Magni P.

ChExVis – Molecular Channel Extraction and Visualization

ChExVis

:: DESCRIPTION

CHEXVIS is a tool for molecular channel extraction and visualization. CHEXVIS supports the visual exploration of multiple channels together with their geometric and physico-chemical properties thereby enabling the understanding of the basic biology of transport through protein channels

::DEVELOPER

Visualization & Graphics Lab, Dept. of Computer Science & Automation, and Chandra Lab, Dept. of Biochemistry.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

CHEXVIS: a tool for molecular channel extraction and visualization
Masood TB, Sandhya S, Chandra N, Natarajan V.
BMC Bioinformatics. 2015 Apr 16;16(1):119.

MyWEST – My Web Extraction Software Tool

MyWEST

:: DESCRIPTION

MyWEST is a software package for effective mining of web interfaced biomolecular databanks. It provides an intuitive visual interface for building templates that define which information should be extracted from HTML pages of web databanks, then uses the created templates to mine information from multiple web pages of different databanks, stores and aggregates in a common database the extracted data, and allows performing articulated queries on the aggregated data for identification of hidden significant biological information.

::DEVELOPER

BioMedical Informatics Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • MS-Access
  • MySQL
  • Excel
  • Java

:: DOWNLOAD

 MyWEST

:: MORE INFORMATION

Citation

Masseroli M, Stella A, Meani N, Alcalay M, Pinciroli F.
MyWEST: My Web Extraction Software Tool for effective mining of annotations from web-based databanks.
Bioinformatics 2004 Dec 12; 20(18): 3326-3335.

EFFECT 2013 – Automated Construction and Extraction of Features for Classification of Biological Sequences

EFFECT 2013

:: DESCRIPTION

EFFECT is an algorithmic framework for automated detection of functional signals in biological sequences.

::DEVELOPER

Computational Biology lab, George Mason University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java
  • BioJava

:: DOWNLOAD

 EFFECT

:: MORE INFORMATION

Citation

Uday Kamath, Kenneth A. De Jong, and Amarda Shehu.
“Effective Automated Feature Construction and Selectionfor Classification of Biological Sequences.”
PLoS One, 2014 (in press).

SubNet 2.0 – Subnetwork Extraction

SubNet 2.0

:: DESCRIPTION

SubNet is a Java-based stand-alone program for extracting subnetworks, given a basal network and a set of selected nodes.

::DEVELOPER

ZDZ lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /Windows / MacOsX
  • Java

:: DOWNLOAD

 SubNet

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Oct 1;29(19):2509-11. doi: 10.1093/bioinformatics/btt430. Epub 2013 Aug 13.
SubNet: a Java application for subnetwork extraction.
Lemetre C1, Zhang Q1, Zhang ZD.

ACME – Automated Cell Morphology Extraction

ACME

:: DESCRIPTION

ACME is a state-of-the-art open-source C++ software for reconstructing membranes to achieve high-quality whole cell segmentations. The software enables the quantification of cell morphologies, cell size, tissue interfaces, arrangement in tightly-packed tissues, and tissue geometry from time-lapse image sequences. The software is generic, modular, scalable to large datasets, and provides an easy API for interfacing with other software systems.

::DEVELOPER

the Megason Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOSX /Linux

:: DOWNLOAD

 ACME

:: MORE INFORMATION

Citation

ACME: Automated Cell Morphology Extractor for Comprehensive Reconstruction of Cell Membranes.
Mosaliganti KR, Noche RR, Xiong F, Swinburne IA, Megason SG.
PLoS Comput Biol. 2012 Dec;8(12):e1002780. doi: 10.1371/journal.pcbi.1002780. Epub 2012 Dec 6.

BioContext 1.0 – System for Extraction and Contextualization of Biomedical Events

BioContext 1.0

:: DESCRIPTION

BioContext is a text mining system for extracting information about molecular processes in biomedical articles.Using the data extracted by BioContext, it is possible to get an overview of a range of biomolecular processes relating to a particular gene or anatomical location.

::DEVELOPER

the Nenadic group & the Bergman lab.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • UCSC tools
  • Python

:: DOWNLOAD

 BioContext

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Aug 15;28(16):2154-61. Epub 2012 Jun 17.
BioContext: an integrated text mining system for large-scale extraction and contextualization of biomolecular events.
Gerner M, Sarafraz F, Bergman CM, Nenadic G.