:: DESCRIPTION
DSM framework is a software of content-based exploration and retrieval method for whole metagenome sequencing samples.
:: DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2014 May 19. pii: btu340. [Epub ahead of print]
Exploration and retrieval of whole-metagenome sequencing samples.
Seth S, Välimäki N, Kaski S, Honkela A.
:: DESCRIPTION
The goal of AGILE (Assembled Genome minIng pipeLinE) is to mine and annotate genes from a target genome using a set of reference genes from a closely related taxon.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Hughes GM, Teeling EC.
AGILE: an assembled genome mining pipeline.
Bioinformatics. 2019 Apr 1;35(7):1252-1254. doi: 10.1093/bioinformatics/bty781. PMID: 30184049.
:: DESCRIPTION
RNAMiner has been developed to convert gigabytes of raw RNA-Seq data into kilobytes of valuable biological knowledge through a five-step data mining and knowledge discovery process.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Li J, Hou J, Sun L, Wilkins JM, Lu Y, et al. (2015)
From Gigabyte to Kilobyte: A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data.
PLoS ONE 10(4): e0125000.
:: DESCRIPTION
@Note is Biomedical Text Mining platform that copes with major Information Retrieval and Information Extraction tasks and promotes multi-disciplinary research. In fact, it aims to provide support to three different usage roles: biologists, text miners and application developers.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Anália Lourenço , Rafael Carreira, Sónia Carneiro, Paulo Maia, Daniel Glez-Peña , Florentino Fdez-Riverola , Eugénio C Ferreira , Isabel Rocha and Miguel Rocha.
@Note: A workbench for Biomedical Text Mining.
Journal of Biomedical Informatics 2009, 42 710-720
:: DESCRIPTION
iPBA is a tool for protein structures mining and superimposition based on similarity in the local backbone conformation.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
iPBA: a tool for protein structure comparison using sequence alignment strategies.
Gelly JC, Joseph AP, Srinivasan N, de Brevern AG.
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W18-23. doi: 10.1093/nar/gkr333.
:: DESCRIPTION
TPM algorithm clusters any time-series data set, specifically iTRAQ LC-MS/MS data sets. The data points that have a similar behavior over the time course are clustered together.
::DEVELOPER
Epithelial Systems Biology Laboratory
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Fahad Saeed, Trairak Pisitkun, Mark Knepper and Jason D Hoffert,
“Mining Temporal Patterns from iTRAQ Mass Spectrometry (LC-MS/MS) Data“,
The Proceedings of the ISCA 3rd International Conference on Bioinformatics and Computational Biology (BiCoB), Vol 1. pp 152-159 New Orleans, Louisiana, USA, March 23-25, 2011 (ISBN: 978-1-880843-81-9)
:: DESCRIPTION
miRNA Digger is a pipeline for large-scale identifiction of the new microRNA genes by screening the cleavage signals resided within the genome.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
miRNA Digger: a comprehensive pipeline for genome-wide novel miRNA mining.
Yu L, Shao C, Ye X, Meng Y, Zhou Y, Chen M.
Sci Rep. 2016 Jan 6;6:18901. doi: 10.1038/srep18901.
:: DESCRIPTION
ArrayMining is a server for automating statistical analysis of gene and protein expression microarray data, designed as a supporting tool for investigation of the genetic components of diseases.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation:
BMC Bioinformatics. 2009 Oct 28;10:358. doi: 10.1186/1471-2105-10-358.
ArrayMining: a modular web-application for microarray analysis combining ensemble and consensus methods with cross-study normalization.
Glaab E, Garibaldi JM, Krasnogor N.
:: DESCRIPTION
NetPathMiner implements a flexible module-based process flow for network path mining and visualization, which can be fully inte-grated with user-customized functions. It supports construction of various types of genome scale networks from three different pathway file formats, enabling its utility to most common pathway databases. In addition, NetPathMiner provides different visualization techniques to facilitate the analysis of even thousands of output paths.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
NetPathMiner: R/Bioconductor package for network path mining through gene expression.
Mohamed A, Hancock T, Nguyen CH, Mamitsuka H.
Bioinformatics. 2014 Jul 28. pii: btu501.
:: DESCRIPTION
NLProt is a tool for finding protein-names in natural language-text. It is based on Support Vector Machines (SVMs), which are trained on contextual-features of named entities in scientific language. Additionally, simple filtering rules and a protein-name dictionary are used to increase performance. NLProt reached a precicion (accuracy) of 70% at a recall (coverage) of 85% after running it on the 166 most recent abstracts of EMBL and Cell
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
NLProt: extracting protein names and sequences from papers.
Mika S, Rost B.
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W634-7.
