Tag: Extraction

Peakhood v0.3 – Individual Site Context Extraction for CLIP-Seq Peak Regions

Peakhood v0.3

:: DESCRIPTION

Peakhood is a tool that takes a set of CLIP-seq peak regions, and for each region individually extracts the most likely site context (transcript or genomic).

::DEVELOPER

Bioinformatics Group Albert-Ludwigs-University Freiburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Conda

:: DOWNLOAD

Peakhood

:: MORE INFORMATION

Citation

Uhl M, Rabsch D, Eggenhofer F, Backofen R.
Peakhood: individual site context extraction for CLIP-seq peak regions.
Bioinformatics. 2021 Nov 4:btab755. doi: 10.1093/bioinformatics/btab755. Epub ahead of print. PMID: 34734974.

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

SubNet

:: 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.

RIscoper – RNA Interaction Extraction from Literatures

RIscoper

:: DESCRIPTION

RIscoper (RNA Interactome Scoper) represents the first tool for full-scale RNA interactome scanning and was developed for extracting RRIs from the literature based on the N-gram model.

::DEVELOPER

WD Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Java

:: DOWNLOAD

RIscoper

:: MORE INFORMATION

Citation

Zhang Y, Liu T, Chen L, Yang J, Yin J, Zhang Y, Yun Z, Xu H, Ning L, Guo F, Jiang Y, Lin H, Wang D, Huang Y, Huang J.
RIscoper: a tool for RNA-RNA interaction extraction from the literature.
Bioinformatics. 2019 Sep 1;35(17):3199-3202. doi: 10.1093/bioinformatics/btz044. PMID: 30668649.

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

Kamath U, De Jong K, Shehu A.
Effective automated feature construction and selection for classification of biological sequences.
PLoS One. 2014 Jul 17;9(7):e99982. doi: 10.1371/journal.pone.0099982. PMID: 25033270; PMCID: PMC4102475.

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

Masseroli Marco, Ph.D

:: SCREENSHOTS

MyWEST

:: 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.

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.

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

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

ArchTEx

:: 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.

Bubble GUM 1.3.19 – Extraction of Phenotype Molecular Signatures and Comprehensive Visualization

Bubble GUM 1.3.19

:: DESCRIPTION

Bubble GUM (GSEA Unlimited Map) is a computational tool that allows to automatically extract phenotype signatures based on transcriptomic data and to perform easily multiple GSEA runs in a row.

::DEVELOPER

Centre d’Immunologie, de Marseille-Luminy

:: SCREENSHOTS

BubbleGUM

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 Bubble GUM

:: MORE INFORMATION

Citation

BubbleGUM: automatic extraction of phenotype molecular signatures and comprehensive visualization of multiple Gene Set Enrichment Analyses.
Spinelli L, Carpentier S, Montañana Sanchis F, Dalod M, Vu Manh TP.
BMC Genomics. 2015 Oct 19;16(1):814. doi: 10.1186/s12864-015-2012-4.