geneid 1.4.4 – Predict Genes in Anonymous Genomic Sequences

geneid 1.4.4

:: DESCRIPTION

geneid is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure. In the first step, splice sites, start and stop codons are predicted and scored along the sequence using Position Weight Arrays (PWAs). In the second step, exons are built from the sites. Exons are scored as the sum of the scores of the defining sites, plus the the log-likelihood ratio of a Markov Model for coding DNA. Finally, from the set of predicted exons, the gene structure is assembled, maximizing the sum of the scores of the assembled exons. geneid offers some type of support to integrate predictions from multiple source via external gff files and the redefinition of the general gene structure or model is also feasible. The accuracy of geneid compares favorably to that of other existing tools, but geneid is likely more efficient in terms of speed and memory usage.

geneid Online

:: DEVELOPER

geneid Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 geneid

:: MORE INFORMATION

Citation:

E. Blanco, G. Parra and R. Guigó,
Using geneid to Identify Genes.”,
Curr Protoc Bioinformatics. 2007 Jun;Chapter 4:Unit 4.3.

BioMyn – Mining Gene and Protein Knowledge

BioMyn

:: DESCRIPTION

BioMyn is a comprehensive online resource that integrates information related to human genes and proteins from over a dozen external databases. It includes Gene Ontology annotations of human genes and proteins, sequence family classifications, protein domain architectures, metabolic and signaling pathways, protein interactions and protein complexes, and disease associations.

::DEVELOPER

Max-Planck-Institut Informatik

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 BioMyn

:: MORE INFORMATION

ProbeLynx 1.2.2 – Update the Association of Microarray Probes to Genes

ProbeLynx 1.2.2

:: DESCRIPTION

ProbeLynx is a web-based tool for updating the association of microarray probes to genes. using the latest genomics sequence information and experimentally determined cross-hybridization cutoffs, ProbeLynx allows users to upload microarray probe sequences to re-examine probe specificity and provide annotation updates relevant to determining which gene(s) and transcript(s) are associated with a given probe.

::DEVELOPER

Brinkman Laboratory, Simon Fraser University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ProbeLynx

:: MORE INFORMATION

Citation

Roche FM, Hokamp K, Acab M, Babiuk LA, Hancock RE, Brinkman FS.
ProbeLynx: a tool for updating the association of microarray probes to genes.
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W471-4. PMID: 15215432

GeneTree 1.3 – Compare Gene and Species Trees

GeneTree 1.3

:: DESCRIPTION

GeneTree is an experimental program for comparing gene and species trees. The program can compute the cost of embedding a gene tree within a species tree, visually display the location and number of gene duplications and losses, and search for optimal species trees.

::DEVELOPER

Professor Rod Page

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / PowerMac

:: DOWNLOAD

GeneTree for win , for Power Macintosh

:: MORE INFORMATION

Citation

R D Page
GeneTree: comparing gene and species phylogenies using reconciled trees.
Bioinformatics. 1998;14(9):819-20.

Orphelia – Predict Genes in Metagenomic Sequencing Reads

Orphelia

:: DESCRIPTION

Orphelia is a metagenomic ORF finding tool for the prediction of protein coding genes in short, environmental DNA sequences with unknown phylogenetic origin [1]. Orphelia is based on a two-stage machine learning approach that was recently introduced by our group. After the initial extraction of open reading frames (ORFs), linear discriminants are used to extract features from those ORFs. Subsequently, an artificial neural network combines the features and computes a gene probability for each ORF in a fragment. A greedy strategy computes a likely combination of high scoring ORFs with an overlap constraint.

Orphelia Online Version

::DEVELOPER

the Department of Bioinformatics of the University of Göttingen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

Orphelia

:: MORE INFORMATION

Citation

K. J. Hoff, T. Lingner, P. Meinicke, M. Tech (2009)
Orphelia: predicting genes in metagenomic sequencing reads
Nucleic Acids Research, 37:W101-W105.

MapMaker 3 – Genetic Linkage Analysis & Mapping Genes Complex Traits

MapMaker 3

:: DESCRIPTION

MapMaker is a package containing a program for genetic linkage analysis and a program for mapping genes underlying complex traits.

MAPMAKER/EXP is a linkage analysis package designed to help construct primary linkage maps of markers segregating in experimental crosses. MAPMAKER/EXP performs full multipoint linkage analysis (simultaneous estimation of all recombination fractions from the primary data) for dominant, recessive, and co-dominant (e.g. RFLP-like) markers. MAPMAKER/EXP is an experimental-cross-only successor to the original MAPMAKER program.

MAPMAKER/QTL is a companion program to MAPMAKER/EXP which allows one to map genes controlling polygenic quantitative traits in F2 intercrosses and BC1 backcrosses relative to a genetic linkage map. More information on MAPMAKER/QTL can be found in the technical report (included with MAPMAKER/QTL).

::DEVELOPER

The Broad Institute, Cambridge, MA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows

:: DOWNLOAD

MapMaker

:: MORE INFORMATION

Citation

Please use Lander et al. 1987 for MAPMAKER/EXP, and Paterson et al. 1988 for
MAPMAKER/QTL. Please also cite:

S. Lincoln, M. Daly, and E. Lander: Constructing Genetic Maps with MAPMAKER/EXP
3.0. (1992) Whitehead Institute Technical Report. 3rd edition.

S. Lincoln, M. Daly, and E. Lander: Mapping Genes Controlling Quantitative
Traits with MAPMAKER/QTL 1.1. (1992) Whitehead Institute Technical Report. 2nd
edition.

TOUR OF THE BASICS – Introduce DNA & Genes

TOUR OF THE BASICS

:: DESCRIPTION

TOUR OF THE BASICS is a flash animated tour of  DNA & Genes.

::DEVELOPER

Genetic Science Learning Center

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OsX

:: DOWNLOAD

TOUR OF THE BASICS for win ; for MacOsX

:: MORE INFORMATION

Funding provided by a grant from The R. Harold Burton Foundation.

 

BootFam – Define Gene/Protein Families

BootFam

:: DESCRIPTION

BootFam takes as input a set of homologous protein sequences, a species tree, and a sequence-to-species mapping. The output is a set of gene families relative to the species tree.

::DEVELOPER

Lars Arvestad

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ windows/MacOsX
  • Perl

:: DOWNLOAD

BootFam Source Code

:: MORE INFORMATION

BootFam is distributed under the GNU General Public License.