DNAlive – Display DNA Structural Features in relation with Genome Annotations and Functions

DNAlive

:: DESCRIPTION

 DNAlive displays DNA structure features in relation with genome annotations and functions.DNAlive is a tool for the analysis of structural and physical characteristics of genomic DNA.

::DEVELOPER

Molecular Modelling & Bioinformatics Unit. IRB Barcelona

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 No

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Aug 1;24(15):1731-2. Epub 2008 Jun 9.
DNAlive: a tool for the physical analysis of DNA at the genomic scale.
Goñi JR, Fenollosa C, Pérez A, Torrents D, Orozco M.

OMIGA 1.0 – Optimized Maker-based Insect Genome Annotation

OMIGA 1.0

:: DESCRIPTION

OMIGA is a pipeline for predicting protein-coding genes from insect genomes

::DEVELOPER

Li Lab: Insect Genomic and Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • mysql(version 5.1 or later versions)
    – abyss(version 1.3.5 or later versions)
    – cegma(version 2.4.0 or later versions)
    – RepeatModeler(version 1.0.5 or later versions)
    – RepeatMasker(version 3.3.0 or later versions)
    – tophat(version 2.0.6 or later versions)
    – Cufflinks(version 2.0.2 or later versions)
    – Augustus(version 2.6.1 or later versions)
    – SNAP(version 2006-07-28 or later versions)
    – GeneMark-es(version 2.3 or later versions)
    – Maker(version 2.26 or later versions)
    – Interproscan(version 4.8 or later versions)

:: DOWNLOAD

 OMIGA

:: MORE INFORMATION

Citation

Mol Genet Genomics. 2014 Aug;289(4):567-73. doi: 10.1007/s00438-014-0831-7. Epub 2014 Mar 9.
OMIGA: Optimized Maker-Based Insect Genome Annotation.
Liu J1, Xiao H, Huang S, Li F.

CpGAVAS 20130506 – Chloroplast Genome Annotation, Visualization, Analysis and GenBank Submission Tool

CpGAVAS 20130506

:: DESCRIPTION

CPGAVAS (Chloroplast Genome Annotation, Visualization, Analysis, and GenBank Submission) is a web server which allows accurate genome annotation, the generation of circular chloroplast genome maps, the provision of useful analysis results of the annotated genome, the creation of files that can be submitted to GenBank directly.

::DEVELOPER

IMP Advanced Genomic Analysis Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Genomics. 2012 Dec 20;13:715. doi: 10.1186/1471-2164-13-715.
CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences.
Liu C, Shi L, Zhu Y, Chen H, Zhang J, Lin X, Guan X.

MetaNetX – Automated Model Construction and Genome Annotation for Large-Scale Metabolic Networks

MetaNetX

:: DESCRIPTION

MetaNetX is a webserver for accessing, analysing and manipulating genome-scale metabolic networks (GSMs) as well as biochemical pathways.

::DEVELOPER

The Swiss Initiative in Systems Biology

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks
Mathias Ganter, Thomas Bernard, Sébastien Moretti, Jörg Stelling and Marco Pagni
Bioinformatics (2013), 29(6):815-816

CGL 0.08 – Library designed to Facilitate the use of Genome Annotation

CGL 0.08

:: DESCRIPTION

CGL (Comparitive Genomics Library) is a software library designed to facilitate the use of genome annotations as substrates for computation and experimentation.The purpose of CGL is to provide an informatics infrastructure for a laboratory, department, or research institute engaged in the large-scale analysis of genomes and their annotations.

::DEVELOPER

Yandell Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CGL

:: MORE INFORMATION

Citation:

Mark Yandell, et al.
Large-Scale Trends in the Evolution of Gene Structures within 11 Animal Genomes
PLoS Comput Biol. 2006 March; 2(3): e15.

Genoman – A Library for Accessing and Manipulating Genome Annotation data

Genoman

:: DESCRIPTION

Genoman (short for genome analysis) is an object-oriented Perl library for accessing and manipulating genome annotation data (e.g. genomic locations of genes and other features, alignments of transcript sequences to a genome, and alignments between different genomes). Genoman defines a set of classes for representing such data. The classes are designed to be flexible and sufficiently efficient to allow their use in analysis pipelines for dealing with large data sets. The library is designed to allow data retrieval from different types of files and databases in a consistent manner, into objects of the same classes. Genoman can be supplemented with custom-written database interface classes for accessing particular databases.

::DEVELOPER

Pär Engström

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Genoman

:: MORE INFORMATION

MADAP 2.0 – Clustering Tool for One-dimensional Genome Annotation Data Mapped onto Genome Sequences

MADAP 2.0

:: DESCRIPTION

MADAP is a flexible clustering tool for the interpretation of one-dimensional genome annotation data mapped onto complete or partial genome sequences. Such data might consist in counts, probabilities, or intensities and be obtained from cDNA and tag sequencing protocols to map the 5′ and 3’ends of mRNA, from ChIP-chip analysis, or from genome-wide SNP-typing used in genotype-phenotype association studies. MADAP identifies groups of data corresponding to one or several genomic sites, and estimates the volume and extension of such groups (clusters).

::DEVELOPER

Computational Cancer Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 MADAP

:: MORE INFORMATION

Citation

Schmid CD, Sengstag T, Bucher P and Delorenzi M. (2007)
MADAP, a flexible clustering tool for the interpretation of one-dimensional genome annotation data.
Nucleic Acids Res, 35, W201-205.

Genquire 3.4.1 /WinGenquire 1.1 – Genome Annotation Workstation

Genquire 3.4.1 /WinGenquire 1.1

:: DESCRIPTION

Genquire is a genome browser and annotation tool based on bioperl and bioperl-gui.The Genquire system is designed to be a standalone genome browser/editor with the ability to connect to one or more genome databases or flat-file data sources and display the information in an interactive graphical display.

::DEVELOPER

Genquire Team

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 GenquireWinGenquire

:: MORE INFORMATION

Citation

M.D. Wilkinson, D. Block and W.L. Crosby
Genquire: genome annotation browser/editor
Bioinformatics (2002) 18 (10): 1398-1399.

PPFINDER 1.0 – Find Processed Pseudogenes in Genome Annotations

PPFINDER 1.0

:: DESCRIPTION

PPFINDER is a Perl-based procedure for finding processed pseudogenes in genome annotations (GTF format). PPFINDER identifies pseudogenes using two different methods, and creates a GTF file with pseudogene coordinates that can be used for masking the genome sequence. In gene prediction mode, PPFINDER will mask out the genomic sequence and rerun gene prediction. Rounds of pseudogene masking and gene prediction are iterated until convergence.

::DEVELOPER

The Brent Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PPFINDER

:: MORE INFORMATION