Projects that are tagged with sequence analysis.


Logo JMLR Sally 0.9.0

by konrad - July 1, 2014, 22:43:51 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 18113 views, 3669 downloads, 2 subscriptions

About: A Tool for Embedding Strings in Vector Spaces

Changes:

Support for hash-based dimension reduction: simhash, minhash and Bloom filter. Support for several n-gram variants: regular, sorted, positional and blended n-grams. Simplified configuration.


Logo Harry 0.2

by konrad - May 3, 2014, 18:48:38 CET [ Project Homepage BibTeX Download ] 1091 views, 234 downloads, 1 subscription

About: A Tool for Measuring String Similarity

Changes:

This release adds support for the Optimal Sequence Alignment distance (OSA) and fixes several minor bugs.


Logo Malheur 0.5.4

by konrad - December 25, 2013, 13:20:31 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 11341 views, 2205 downloads, 1 subscription

About: Automatic Analysis of Malware Behavior using Machine Learning

Changes:

Support for new version of libarchive. Minor bug fixes.


Logo Salad 0.4.2

by chwress - December 25, 2013, 08:00:12 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 2404 views, 457 downloads, 1 subscription

About: A Content Anomaly Detector based on n-Grams

Changes:

Fixes a bug in the unit testing framework on Windows


Logo BCILAB 1.0-beta

by chkothe - January 6, 2012, 23:47:55 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 2897 views, 595 downloads, 1 subscription

About: MATLAB toolbox for advanced Brain-Computer Interface (BCI) research.

Changes:

Initial Announcement on mloss.org.


Logo Sequin v1.1.0.0

by apitman - September 23, 2011, 11:47:53 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 3564 views, 866 downloads, 1 subscription

About: Sequin is an open source sequence mining library written in C#.

Changes:

Sequin v1.1.0.0 released


Logo pHMM4weka 1.0

by smm52 - October 22, 2010, 03:48:07 CET [ Project Homepage BibTeX Download ] 3020 views, 888 downloads, 1 subscription

About: This Java software implements Profile Hidden Markov Models (PHMMs) for protein classification for the WEKA workbench. Standard PHMMs and newly introduced binary PHMMs are used. In addition the software allows propositionalisation of PHMMs.

Changes:

description changed


Logo LSTM for biological sequence analysis 1.0

by mhex - July 28, 2010, 16:32:29 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 5123 views, 1193 downloads, 1 subscription

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About: Implementation of LSTM for biological sequence analysis (classification, regression, motif discovery, remote homology detection). Additionally a LSTM as logistic regression with spectrum kernel is included.

Changes:

Spectrum LSTM package included


Logo svmPRAT 1.0

by rangwala - December 28, 2009, 00:27:03 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 3560 views, 880 downloads, 1 subscription

About: BACKGROUND:Over the last decade several prediction methods have been developed for determining the structural and functional properties of individual protein residues using sequence and sequence-derived information. Most of these methods are based on support vector machines as they provide accurate and generalizable prediction models. RESULTS:We present a general purpose protein residue annotation toolkit (svmPRAT) to allow biologists to formulate residue-wise prediction problems. svmPRAT formulates the annotation problem as a classification or regression problem using support vector machines. One of the key features of svmPRAT is its ease of use in incorporating any user-provided information in the form of feature matrices. For every residue svmPRAT captures local information around the reside to create fixed length feature vectors. svmPRAT implements accurate and fast kernel functions, and also introduces a flexible window-based encoding scheme that accurately captures signals and pattern for training eective predictive models. CONCLUSIONS:In this work we evaluate svmPRAT on several classification and regression problems including disorder prediction, residue-wise contact order estimation, DNA-binding site prediction, and local structure alphabet prediction. svmPRAT has also been used for the development of state-of-the-art transmembrane helix prediction method called TOPTMH, and secondary structure prediction method called YASSPP. This toolkit developed provides practitioners an efficient and easy-to-use tool for a wide variety of annotation problems. Availability: http://www.cs.gmu.edu/~mlbio/svmprat/

Changes:

Initial Announcement on mloss.org.


Logo MALLET 2.0-rc4

by jacktanner - August 24, 2009, 23:10:14 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 10097 views, 1613 downloads, 1 subscription

About: MALLET is a Java-based package for statistical natural language processing, document classification, clustering, topic modeling, information extraction, and other machine learning applications to [...]

Changes:

MALLET 2.0 RC4 Release Notes July 16, 2009

Major updates:

An implementation of generalized expectation criteria training of MaxEnt classifiers and methods for obtaining constraints (c.f. Gregory Druck, Gideon Mann, Andrew McCallum "Learning from Labeled Features using Generalized Expectation Criteria.")

PagedInstanceList has been substantially rewritten by Mike Bond.

Bug fixes to topic model hyperparameter optimization and topic inference.


Logo FlexCRFs 0.3

by pxhieu - May 10, 2008, 09:24:54 CET [ Project Homepage BibTeX Download ] 4754 views, 2612 downloads, 1 subscription

About: FlexCRFs is a conditional random field toolkit for segmenting and labeling sequence data written in C/C++ using STL library. It was implemented based on the theoretic model presented in (Lafferty et [...]

Changes:

Initial Announcement on mloss.org.


Logo Local Alignment Kernels 0.3.2

by hiroto - December 1, 2007, 00:10:23 CET [ Project Homepage BibTeX Download ] 5213 views, 1221 downloads, 0 subscriptions

About: Local alignment kernels measure the similarity between two sequences by summing up scores obtained from local alignments with gaps of the sequences.

Changes:

Initial Announcement on mloss.org.


About: PALMA computes the optimal spliced alignment of a mRNA sequence to a genomic sequence. The main python script takes two FASTA files containing the target (e.g. a DNA sequence, part of the genome) [...]

Changes:

Initial Announcement on mloss.org.


Logo Lush 1.2.1

by ylecun - November 12, 2007, 06:35:08 CET [ Project Homepage BibTeX Download ] 4781 views, 2127 downloads, 0 subscriptions

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About: Lush is an object-oriented Lisp dialect with a super-simple way of integrating C/C++ code and libraries. It includes extensive libraries for numerical computing, machine learning, and computer [...]

Changes:

Initial Announcement on mloss.org.