Glimmer 3.02b / GlimmerM 2.5.1 – Microbial Gene-finding System

Glimmer 3.02b / GlimmerM 2.5.1

:: DESCRIPTION

Glimmer (Gene Locator and Interpolated Markov ModelER) is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. Glimmer uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA.

GlimmerM is a gene finder derived from Glimmer, but developed specifically for eukaryotes. It is based on a dynamic programing algorithm that considers all combinations of possible exons for inclusion in a gene model and chooses the best of these combinations.

::DEVELOPER

the Center for Bioinformatics and Computational Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Mac OsX

:: DOWNLOAD

Glimmer , GlimmerM

:: MORE INFORMATION

Citation:

A.L. Delcher, D. Harmon, S. Kasif, O. White, and S.L. Salzberg. Improved microbial gene identification with GLIMMER, Nucleic Acids Research 27:23 (1999), 4636-4641.
S. Salzberg, A. Delcher, S. Kasif, and O. White. Microbial gene identification using interpolated Markov models, Nucleic Acids Research26:2 (1998), 544-548.
A.L. Delcher, K.A. Bratke, E.C. Powers, and S.L. Salzberg. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics(Advance online version) (2007).

Pertea, M. and Salzberg, S.L.
Using GlimmerM to find genes in eukaryotic genomes.
Current Protocols in Bioinformatics, 2002.

Microtaxi – Microbial Taxonomic Identification and Classification Server

Microtaxi

:: DESCRIPTION

Microtaxi uses an taxon-specific gene based approach and provides an alternate valuable methodology to carry out the taxonomic classification of newly sequenced or existing bacterial genomes.

::DEVELOPER

MetaBioSys laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Perl

:: DOWNLOAD

Microtaxi

:: MORE INFORMATION

Citation

BMC Genomics. 2015 May 20;16:396. doi: 10.1186/s12864-015-1542-0.
Using the taxon-specific genes for the taxonomic classification of bacterial genomes.
Gupta A, Sharma VK

CRITICA 1.05 – Microbial Gene Finder

CRITICA 1.05

:: DESCRIPTION

CRITICA (Coding Region Identification Tool Invoking Comparative Analysis) is a microbial gene finder that combines traditional approaches to the problem with a novel comparative analysis. If, in a nucleotide alignment, a pair of ORFs can be found in which the conceptual translated products are more conserved than would be expected from the amount of conservation at the nucleotide level, this is evolutionary evidence that the DNA sequences are protein coding. Regions found by this method are used to generate traditional dicodon frequencies for further analysis. CRITICA thus is not dependent on (often erroneous) sequence annotations, which many other algorithms base their training sets upon, and uses comparative information in a more biologically meaningful way than a simple similarity search. CRITICA was used in the Archeoglobus fulgidus and Aquifex aeolicus genome projects and is still in use by several groups

::DEVELOPER

Dr. Jonathan Badger

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

CRITICA

:: MORE INFORMATION

Citation:

Jonathan H. Badger, Gary J. Olsen.
CRITICA: Coding Region Identification Tool Invoking Comparative Analysis.
Molecular Biology and Evolution, 16(4):512-524. 1999.