Tag: Gene

Exalign 1.0 – Gene Structural Alignments and Database Search

Exalign 1.0

:: DESCRIPTION

Exalign is a tool that performs alignments of gene exonic structures. In particular it works by aligning arrays representing the exon lengths of genes. While the aligning algorithms used by Exalign are the well known Smith-Waterman and Needleman-Wunsch ones (with a suitable scoring function), the program performs a post-processing step that tries to identify intron gain/loss events (see sections about exon merging).

::DEVELOPER

Bioinformatics Evolution @nd COmparative geNomics lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C++ Complier

:: DOWNLOAD

 Exalign

:: MORE INFORMATION

Citation:

Pavesi G, Zambelli F, Caggese C, Pesole G.
Exalign: a new method for comparative analysis of exon-intron gene structures.
Nucleic Acids Res. 2008 May;36(8):e47. Epub 2008 Apr 8.

GPX – Gene Phylogeny eXplorer

GPX

:: DESCRIPTION

GPX (Gene Phylogeny eXplorer) is a web-based tool that facilitates comparative genome analysis of different species. GPX displays results as an interactive map that allows users to explore and interpret genomic data representing gene evolution. It allows the visualization of consensus and conflicting evolutionary histories of genes.

::DEVELOPER

Lutz Hamel , Gogarten Lab 

:: SCREENSHOTS

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 No

:: MORE INFORMATION

Citation

Nahar, Neha, Poptsova, Maria S., Hamel, Lutz, and Gogarten, J. Peter (2007)
GPX: A Tool for the Exploration and Visualization of Genome Evolution.
Proceedings of the IEEE 7th International Symposium on Bioinformatics & Bioengineering (BIBE07) Boston, pp1338 – 1342,

Moara 1.0.6 – Extract & Normalize Gene and Protein Mentions

Moara 1.0.6

:: DESCRIPTION

Moara is a software for gene mentions and normalization in biological texts.

::DEVELOPER

Moara team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Windows/Linux/MacOsX
  • Java
  • MySQL
  • Weka
  • SecondString
  • ABNER

:: DOWNLOAD

 Moara

:: MORE INFORMATION

Citation

Moara: a Java library for extracting and normalizing gene and protein mentions.
Neves ML, Carazo JM, Pascual-Montano A.
BMC Bioinformatics. 2010 Mar 26;11:157.

GUILD – Genes Underlying Inheritance Linked Disorders framework

GUILD

:: DESCRIPTION

GUILD (Genes Underlying Inheritance Linked Disorders) is a network-based prioritization framework to unveil genes associated with a disease phenotype (disease-genes). The sofware exploits several communication mechanisms between disease-genes emerging from the topology of the interaction network. GUILD consists of implementations of 8 algorithms: NetScore, NetZcore, NetShort, NetCombo, fFlow, NetRank, NetWalk and NetProp.

::DEVELOPER

Structural BioInformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R package

:: DOWNLOAD

  GUILD

:: MORE INFORMATION

Citation

Guney E, Oliva B.
Exploiting Protein-Protein Interaction Networks for Genome-wide Disease-Gene Prioritization.
PLoS ONE, 2012, 7(9): e43557.

CarGene 1.0 – Characterization of Sets of Genes based on Metabolic Pathways Analysis

CarGene 1.0

:: DESCRIPTION

CarGene (Charac- terization of Genes) is a software tool, named that helps scientists to validate sets of genes by us- ing the biological knowledge on metabolic pathways stored in the Kyoto Encyclopedia of Genes and Genomes (Kegg), and providing a friendly graphical environment to analyze and compare results generated by dif- ferent clustering and/or biclustering techniques. CarGene is based on the degree of coherence of genes in (bi)clusters with respect to metabolic pathways of organisms stored in Kegg, and provides an estimate of obtaining results by chance, including two statistical corrections (Bon- ferroni, and Westfall and Young). One of the most important features of CarGene is the possibility of simultaneously comparing and statis- tically analyzing the information about many groups of genes in both visual and textual manner. Furthermore, it includes its own web browser to explore in detail the information extracted from Kegg. To show the functionality of CarGene, a test based on the study carried out by Huttenshower et al. is performed.

::DEVELOPER

The Bioinformatics group of Seville(Spain)

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows
:: DOWNLOAD

 CarGene

:: MORE INFORMATION

Citation

Int J Data Min Bioinform. 2011;5(5):558-73.
CarGene: characterisation of sets of genes based on metabolic pathways analysis.
Aguilar-Ruiz JS, Rodriguez-Baena DS, Diaz-Diaz N, Nepomuceno-Chamorro IA.

GenePro 2.5.2 – Visualization and Analysis of Protein and Gene Interaction Networks

GenePro 2.5.2.

:: DESCRIPTION

GenePro is a Cytoscape plug-in for the visualization and analysis of protein and gene interaction networks at multiple levels of resolution.

::DEVELOPER

The Wodak Lab

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 GenePro

:: MORE INFORMATION

Citation

Vlasblom, J. et al.
GenePro: a cytoscape plug-in for advanced visualization and analysis of interaction networks.
Bioinformatics 22(17):2178-9 (2006).

Rankgene 1.1 – Rank Genes from Expression data

Rankgene 1.1

:: DESCRIPTION

 Rankgene is a program for analyzing gene expression data, feature selection and ranking genes based on the predictive power of each gene to classify samples into functional or disease categories.

::DEVELOPER

Computational Genomics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Rankgene

:: MORE INFORMATION

Citation:

RankGene: identification of diagnostic genes based on expression data.
Su Y, Murali TM, Pavlovic V, Schaffer M, Kasif S.
Bioinformatics. 2003 Aug 12;19(12):1578-9.

FastER 1.0 – Identification of Genes with Fast-evolving Regions in closely related Genomes

FastER 1.0

:: DESCRIPTION

FastER is a software for identifying orthologous gene pairs that appear to have fast-evolving regions between two closely related genomes. Its input can be either two closely related whole genome sequences or two closely related orthologous sequences. It consists of two steps: first, it will detect all regions with overrepresented nonsynonymous mutations; second, it will test the nonsynonymous evolution rate against the neutral evolution rate in that gene.

::DEVELOPER

Computational Genomics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 FastER

:: MORE INFORMATION

Citation:

Identification of genes with fast-evolving regions in microbial genomes
Yu Zheng, Richard J. Roberts and Simon Kasif
Nucl. Acids Res. (2004) 32 (21): 6347-6357.

MCDGPA – Modularized Candidate Disease Genes Prioritization Algorithm

MCDGPA

:: DESCRIPTION

MCDGPA is proposed to identify disease-related genes. MCDGPA is divided into three steps: module partition, genes prioritization in each disease-associated module, and rank fusion for the global ranking. When applied to the prostate cancer and breast cancer network, MCDGPA significantly improves previous algorithms in terms of cross-validation and disease-related genes prediction. In addition, the improvement is robust to the selection of gene prioritization methods when implementing prioritization in each disease-associated module and module partition algorithms when implementing network partition. In this sense MCDGPA is a general framework that allows integrating many previous gene prioritization methods and improving predictive accuracy.

::DEVELOPER

APORC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Matlab

:: DOWNLOAD

  MCDGPA

:: MORE INFORMATION

Citation

Chen X, Yan GY, Liao XP (2010)
A novel candidate disease genes prioritization method based on module partition and rank fusion.
OMICS 4: 337-356.

HCGene 1.0.1 – Hierarchical Classification of Genes

HCGene 1.0.1

:: DESCRIPTION

HCGene (Hierarchical Classification of Genes) implements methods to process and analyze the Gene Ontology (GO) and the FunCat taxonomy in order to support the functional classification of genes.

::DEVELOPER

Giorgio Valentini , Nicolò Cesa-Bianchi

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 HCGene

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Mar 1;24(5):729-31. Epub 2008 Jan 18.
HCGene: a software tool to support the hierarchical classification of genes.
Valentini G, Cesa-Bianchi N.

 

Exit mobile version