:: DESCRIPTION
The GHMM is a freely available C library implementing efficient data structures and algorithms for basic and extended HMMs with discrete and continous emissions.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2011 Nov 2;12:428.
Fast MCMC sampling for hidden Markov Models to determine copy number variations.
Mahmud MP, Schliep A.
:: DESCRIPTION
GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM). Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models . Currently, GlimmerHMM’s GHMM structure includes introns of each phase, intergenic regions, and four types of exons (initial, internal, final, and single).
::DEVELOPER
the Center for Bioinformatics and Computational Biology
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
GlimmerHMM is OSI Certified Open Source Software .
Citation:
Majoros, W.H., Pertea, M., and Salzberg, S.L. TigrScan and GlimmerHMM: two open-source ab initio eukaryotic gene-finders Bioinformatics 20 2878-2879.
:: DESCRIPTION
GQL (Graphical Query Language) is a suite of tools for analyizing time-course experiments. Currently, it is adapted to gene expression data. The two main tools are GQLQuery, for querying data sets, and GQLCluster, which provides a way for computing groupings based on a number of methods (model-based clustering using HMMs as cluster models and estimation of a mixture of HMMs).
::DEVELOPER
Alexander Schliep’s group for bioinformatics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2005 May 15;21(10):2544-5. Epub 2005 Feb 8.
The Graphical Query Language: a tool for analysis of gene expression time-courses.
Costa IG, Schönhuth A, Schliep A.
:: DESCRIPTION
GeneZilla (formerly known as TIGRscan) is a state-of-the-art program for computational prediction of protein-coding genes in eukaryotic DNA, and is based on the Generalized Hidden Markov Model (GHMM) framework, similar to GENSCAN and GENIE. It is highly reconfigurable and includes software for retraining by the end-user. Graph-theoretic representations of the high scoring open reading frames are provided, allowing for exploration of sub-optimal gene models. It utilizes Interpolated Markov Models (IMMs), Maximal Dependence Decomposition (MDD), and includes states for signal peptides, branch points, TATA boxes, CAP sites, and will soon model CpG islands as well.
::DEVELOPER
Bill Majoros, now at Duke University.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
GeneZilla is available for download as OSI Certified Open Source Software under the Artistic License.
Citation:
Majoros W, et al. (2004) TIGRscan and GlimmerHMM: two open-source ab initio eukaryotic gene finders, Bioinformatics 20, 2878-2879.
:: DESCRIPTION
ExAlt is a software program designed to predict alternatively spliced overlapping exons in genomic sequence. The program works in several ways depending on the available input. ExAlt can use information about existing gene structure as well as sequence conservation to improve the precision of its predictions. ExAlt can also make predictions when only a single genomic sequence is available.
::DEVELOPER
Jonathan E. Allen at the Center for Bioinformatics and Computational Biology
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
The ExAlt software is OSI Certified Open Source Software.
Citation:
J. E. Allen and S. L. Salzberg. A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons.Algorithms for Molecular Biology, 1:14, 2006.
