GlimmerHMM 3.0.4 – Eukaryotic Gene Finder based on GHMM

GlimmerHMM 3.0.4

:: 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

  • Linux / Sun Solaris / Alpha OSF1

:: DOWNLOAD

 GlimmerHMM

:: 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.

GQL 1.0 – GHMM-based tool for Querying and Clustering Gene-Expression time-course data

GQL 1.0

:: 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

 GQL

:: 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.

GHMM 0.9 – General Hidden Markov Model library

GHMM 0.9

:: 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

Alexander Schliep’s group for bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 GHMM

:: 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.

 

GeneZilla 1.22 – GHMM Eukaryotic Gene Finder

GeneZilla 1.22

:: 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

  • Linux / Mac OsX

:: DOWNLOAD

GeneZilla

:: 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 findersBioinformatics 20, 2878-2879.

ExAlt 1.0 – Alternative Exon Isoform Prediction

ExAlt 1.0

:: 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

ExAlt

:: 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.