Projects that are tagged with sequence analysis.


Logo Harry 0.4.2

by konrad - April 16, 2016, 10:50:38 CET [ Project Homepage BibTeX Download ] 8464 views, 1875 downloads, 3 subscriptions

About: A Tool for Measuring String Similarity

Changes:

This release fixes the incorrect implementation of the bag distance.


Logo Salad 0.6.0

by chwress - December 1, 2015, 16:17:35 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 10281 views, 1939 downloads, 3 subscriptions

About: A Content Anomaly Detector based on n-Grams

Changes:

After a full year of development we proudly present you several new features, plenty of bug fixes and better performance :)

  • It now is possible to process data on bit granularity salad [train|inspect] --binary
  • Performance improvements while simultaneously preserving and further advancing readability of the source code.
  • Suppress the verbose output of Salad salad [train|predict] -q
  • Extend the (unit) testing framework to support test of the overall application and memchecks using valgrind.
  • Testing mode was renamed: salad dbg -> salad test
  • Allow to select either client or server-side data when processing network communication.
  • libfoodstoragebox A library encapsulating advanced data structures such as bloom filters.
  • Fixes for a critical bug when using group input and several minor issues.
  • An optionally compressed, text-based model file format salad train -F (txt|archive)
  • The default hashset ('simple2') makes use of djb2 hash
  • Flawless builds using gcc, mingw and clang

Logo KeBABS 1.4.1

by UBod - November 3, 2015, 11:33:46 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 12037 views, 2242 downloads, 3 subscriptions

About: Kernel-Based Analysis of Biological Sequences

Changes:
  • new method to compute prediction profiles from models trained with mixture kernels
  • correction for position specific kernel with offsets
  • corrections for prediction profile of motif kernel
  • additional hint on help page of kbsvm

Logo JMLR Sally 1.0.0

by konrad - March 26, 2015, 17:01:35 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 37871 views, 7364 downloads, 3 subscriptions

About: A Tool for Embedding Strings in Vector Spaces

Changes:

Support for explicit selection of granularity added. Several minor bug fixes. We have reached 1.0


Logo Malheur 0.5.4

by konrad - December 25, 2013, 13:20:31 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 18218 views, 3491 downloads, 1 subscription

About: Automatic Analysis of Malware Behavior using Machine Learning

Changes:

Support for new version of libarchive. Minor bug fixes.


Logo BCILAB 1.0-beta

by chkothe - January 6, 2012, 23:47:55 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 5409 views, 1161 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 ] 5894 views, 1427 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 ] 4690 views, 1381 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 ] 7900 views, 1910 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 ] 5126 views, 1284 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 ] 13601 views, 2242 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 ] 5972 views, 3131 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 ] 6651 views, 1630 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 ] 6235 views, 2623 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.