:: DESCRIPTION
T-WPPDC is a minimally parameterized algorithm for both pattern discovery and sequence classification that directly incorporates positional information.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2011 Aug 1;27(15):2054-61. doi: 10.1093/bioinformatics/btr353. Epub 2011 Jun 17.
A tree-based approach for motif discovery and sequence classification.
Yan R1, Boutros PC, Jurisica I.
:: DESCRIPTION
Oasis is a web application that allows for the fast and flexible online analysis of small-RNA-seq (sRNA-seq) data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Oasis: online analysis of small RNA deep sequencing data.
Capece V, Vizcaino JC, Vidal R, Rahman RU, Centeno TP, Shomroni O, Suberviola I, Fischer A, Bonn S.
Bioinformatics. 2015 Feb 19. pii: btv113.
:: DESCRIPTION
Hetero-RP (Heterogeneity Rescaling Pursuit) is a scalable and tuning-free preprocessing framework, which weighs important features more highly than less important ones in accord with implicitly existing auxiliary knowledge.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Lu YY, Lv J, Fuhrman JA, Sun F.
Towards enhanced and interpretable clustering/classification in integrative genomics.
Nucleic Acids Res. 2017 Nov 16;45(20):e169. doi: 10.1093/nar/gkx767. PMID: 28977511; PMCID: PMC5714251.
:: DESCRIPTION
EukRep is a k-mer-based strategy, for eukaryotic sequence identification and applied it to environmental samples to show that it enables genome recovery, genome completeness evaluation, and prediction of metabolic potential.
::DEVELOPER
:: SCREENSHOTS
N/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
West PT, Probst AJ, Grigoriev IV, Thomas BC, Banfield JF.
Genome-reconstruction for eukaryotes from complex natural microbial communities.
Genome Res. 2018 Apr;28(4):569-580. doi: 10.1101/gr.228429.117. Epub 2018 Mar 1. PMID: 29496730; PMCID: PMC5880246.
:: DESCRIPTION
miRClassify is a novel machine learning-based web server which can rapidly identify miRNA from the primary sequence and classify it into a miRNA family in regardless of similarity in sequence and structure.
::DEVELOPER
Data Mining Group, Xiamen University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Quan Zou*, Yaozong Mao, Lingling Hu, Yunfeng Wu, Zhiliang Ji*.
miRClassify: An advanced web server for miRNA family classification and annotation.
Computers in Biology and Medicine. 2014, 45:157-160.
:: DESCRIPTION
CARROT is a tool for relationship inference that leverages linkage disequilibrium to differentiate between rotated relationships, such as (first-, second-, etc) uncle-niece.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2011 Jul 1;27(13):i333-41. doi: 10.1093/bioinformatics/btr243.
Reconstruction of genealogical relationships with applications to Phase III of HapMap.
Kyriazopoulou-Panagiotopoulou S, Kashef Haghighi D, Aerni SJ, Sundquist A, Bercovici S, Batzoglou S.
:: DESCRIPTION
SCIPHY is a software of tree construction and subfamily detection. It is the key downloadable code from the PhyloFacts repository.
::DEVELOPER
the Berkeley Phylogenomics Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Automated protein subfamily identification and classification.
Brown DP, Krishnamurthy N, Sjölander K.
PLoS Comput Biol. 2007 Aug;3(8):e160.
:: DESCRIPTION
CancerIN is a web server developed for predicting anticancer activity of molecules. Similarity based approach has been used for discrimination or classification of anticancer and non-anticancer molecule.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Prediction of anticancer molecules using hybrid model developed on molecules screened against NCI-60 cancer cell lines.
Singh H, Kumar R, Singh S, Chaudhary K, Gautam A, Raghava GP.
BMC Cancer. 2016 Feb 9;16:77. doi: 10.1186/s12885-016-2082-y.
:: DESCRIPTION
The R package msgl (multinomial sparse group lasso) fits multinomial models for e.g. multiclass classification with a sparse group lasso penalty.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2014 May 15;30(10):1417-23. doi: 10.1093/bioinformatics/btu044. Epub 2014 Jan 24.
Modeling tissue contamination to improve molecular identification of the primary tumor site of metastases.
Vincent M1, Perell K, Nielsen FC, Daugaard G, Hansen NR.
:: DESCRIPTION
R-SVM is a SVM-based method for doing supervised pattern recognition(classification) with microarray gene expression data. The method uses SVM for both classification and for selecting a subset of relevant genes according to their relative contribution in the classification. This process is done recursively so that a series of gene subsets and classification models can be obtained in a recursive manner, at different levels of gene selection. The performance of the classification can be evaluated either on an independent test data set or by cross validation on the same data set. R-SVM also includes an option for permutation experiments to assess the significance of the performance.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
ZHANG, X.G., LU, X., (Joint First Author) XU, X.Q., LEUNG, H.E., WONG, W.H. and LIU, J.S. (2006)
RSVM: A SVM based Strategy for Recursive Feature Selection and Sample Classification with Proteomics Mass-Spectrometry Data.
BMC Bioinformatics, 7:197
