Projects that are tagged with sequence analysis.


Logo KeBABS 1.2.3

by UBod - May 26, 2015, 10:55:44 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 5694 views, 997 downloads, 3 subscriptions

About: Kernel-Based Analysis of Biological Sequences

Changes:
  • new export kebabsCollectInfo for collection of package info
  • update of version dependency to Biostrings, XVector, S4Vector
  • correction for leading + or - in factor label
  • change of bibtex style sheet in vignette to plainnat.bst

Logo Harry 0.4.0

by konrad - March 30, 2015, 14:03:12 CET [ Project Homepage BibTeX Download ] 4943 views, 1071 downloads, 2 subscriptions

About: A Tool for Measuring String Similarity

Changes:

The new release supports measuring string similarity at the granularity of bytes, bits and tokens. A Python interface has been added. Several minor bugs have been fixed.


Logo JMLR Sally 1.0.0

by konrad - March 26, 2015, 17:01:35 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 29154 views, 5715 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 Salad 0.5.0

by chwress - August 22, 2014, 17:54:56 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 6675 views, 1236 downloads, 1 subscription

About: A Content Anomaly Detector based on n-Grams

Changes:

Lots and lots of cool new features and bugfixes ;)

  • Refinements to the user interface: This includes a progress indicator, colors, etc.
  • Determine the expected error (salad-inspect)
  • Enable the user to echo the used parametrization: salad [train|predict|inspect] --echo-params
  • Allow to set the input batch size as program argument: salad [train|predict|inspect] --batch-size
  • libsalad: The library allows to access salad's basic functions
  • Installers and precompiled binaries: Windows installer, Debian (ppa:chwress/salad) & RPM packages as well a generic linux installers.
  • Various minor bug fixes
  • Support for "length at end" zip files
  • Improve salad's usage in a 2-class setting: salad [train|predict|inspect] --input-filter

Logo Malheur 0.5.4

by konrad - December 25, 2013, 13:20:31 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 15359 views, 2944 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 ] 4448 views, 927 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 ] 4889 views, 1177 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 ] 3905 views, 1210 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 ] 6780 views, 1630 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 ] 4405 views, 1137 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 ] 12053 views, 1958 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 ] 5445 views, 2883 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 ] 6014 views, 1466 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 ] 5625 views, 2417 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.