CRIMSON 2.1.3 beta
:: DESCRIPTION
Crimson facilitates the extraction of sub-trees from very large phylogenetic trees.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
- Linux/ MacOsX/ Windows
- java
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Crimson facilitates the extraction of sub-trees from very large phylogenetic trees.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: 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
:: DOWNLOAD
:: 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.
:: DESCRIPTION
SubNet is a Java-based stand-alone program for extracting subnetworks, given a basal network and a set of selected nodes.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: DOWNLOAD
:: 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.
:: 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
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: DOWNLOAD
:: 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.
:: 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
:: DOWNLOAD
:: 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
:: 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
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: REQUIREMENTS
:: DOWNLOAD
:: 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.