Tag: Gene Structure

ParsEval 0.9.2 – Compare Two Sets of Gene Structure Annotations

ParsEval 0.9.2

:: DESCRIPTION

ParsEval is a program for comparing two sets of gene structure annotations (provided as GFF3 files) for the same genomic region. Comparison statistics are calculated for each genic region, as well as for the entire region overall.

::DEVELOPER

The Brendel Group @ Indiana University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

ParsEval

:: MORE INFORMATION

Citation

Standage, D.S. & Brendel, V.P. (2011)
ParsEval: parallel comparison and analysis of gene structure annotations
BMC Bioinformatics 2012, 13:187

yrGATE 2.0.1 – Gene Structure Annotation Tool

yrGATE 2.0.1

:: DESCRIPTION

yrGATE (Your Gene structure Annotation Tool for Eukaryotes) is a web-based gene-structure annotation tool for the identification and dissemination of eukaryotic genes.yrGATE provides an Annotation Tool and Community Utilities for worldwide web-based community genome and gene annotation. Annotators can evaluate gene structure evidence derived from multiple sources to create gene structure annotations. Administrators regulate the acceptance of annotations into published gene sets. yrGATE is designed to facilitate rapid and accurate annotation of emerging genomes as well as to confirm, refine, or correct currently published annotations. yrGATE is highly portable and supports different standard input and output formats.

::DEVELOPER

The Brendel Group @ Indiana University

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

yrGATE

:: MORE INFORMATION

Citation

Wilkerson, M.D., Schlueter, S.D. & Brendel, V. (2006)
yrGATE: a web-based gene-structure annotation tool for the identification and dissemination of eukaryotic genes.
Genome Biol. 7, R58.

GenePainter 2.0.5 – Mapping Gene Structures onto Protein Multiple Sequence Alignment

GenePainter 2.0.5

:: DESCRIPTION

GenePainter is a standalone tool for mapping gene structures onto protein multiple sequence alignments (MSA). Gene structures, as provided by WebScipio, are aligned with respect to the exact positions of the introns (down to nucleotide level) and intron phase. Output can be viewed in various formats, ranging from plain text to graphical output formats.

::DEVELOPER

kollmar_group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Ruby

:: DOWNLOAD

  GenePainter

:: MORE INFORMATION

Citation

S. Mühlhausen, M. Hellkamp & M. Kollmar (2014)
GenePainter 2.0 resolves the taxonomic distribution of intron positions.
Bioinformatics, pii: btu798

Björn Hammesfahr †, Florian Odronitz †, Stefanie Mühlhausen, Stephan Waack & Martin Kollmar (2013)
GenePainter: a fast tool for aligning gene structures of eukaryotic protein families, visualizing the alignments and mapping gene structures onto protein structures.
BMC Bioinformatics 14, 77.

PASA v2.4.1 – Gene Structure Annotation & Analysis

PASA v2.4.1

:: DESCRIPTION

PASA (Program to Assemble Spliced Alignments) is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation consistent with the most recently available experimental sequence data. PASA also identifies and classifies all splicing variations supported by the transcript alignments.

::DEVELOPER

J. Craig Venter Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

PASA

:: MORE INFORMATION

Citation:

Haas, B.J., Delcher, A.L., Mount, S.M., Wortman, J.R., Smith Jr, R.K., Jr., Hannick, L.I., Maiti, R., Ronning, C.M., Rusch, D.B., Town, C.D. et al. (2003)
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies.
Nucleic Acids Res, 31, 5654-5666.

GSDS 2.0 – Gene Structure Display Server

GSDS 2.0

:: DESCRIPTION

GSDS is designed for the visualization of annotated features for genes, and the generation of high-quality figures for publication.

::DEVELOPER

Gao Lab, Peking University.

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

GSDS 2.0: an upgraded gene feature visualization server.
Hu B, Jin J, Guo AY, Zhang H, Luo J, Gao G.
Bioinformatics. 2014 Dec 10. pii: btu817

GENSCAN 20030218 – Identification of complete Gene Structures in Genomic DNA

GENSCAN 20030218

:: DESCRIPTION

GENSCAN identifies complete exon/intron structures of genes in genomic DNA. Novel features of the program include the capacity to predict multiple genes in a sequence, to deal with partial as well as complete genes, and to predict consistent sets of genes occurring on either or both DNA strands. GENSCAN is shown to have substantially higher accuracy than existing methods when tested on standardized sets of human and vertebrate genes, with 75 to 80% of exons identified exactly. The program is also capable of indicating fairly accurately the reliability of each predicted exon

GENSCAN Online Version

::DEVELOPER

Christopher Burge Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GENSCAN

:: MORE INFORMATION

Citation

Prediction of complete gene structures in human genomic DNA.
Burge C, Karlin S.
J Mol Biol. 1997 Apr 25;268(1):78-94.

GenomeScan 1.0 – Prediction of Gene Structures in Genomic Sequences

GenomeScan 1.0

:: DESCRIPTION

GenomeScan is a program for identifying the exon-intron structures of genes in genomic DNA sequences from a variety of organisms, with a focus on human and other vertebrates.  The algorithm combines two principal sources of information: 1) models of exon-intron and splice signal composition; and 2) sequence similarity information such as BLASTX hits.

::DEVELOPER

Christopher Burge Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Yeh, R.-F., Lim, L. P., and Burge, C. B. (2001)
Computational inference of homologous gene structures in the human genome.
Genome Res. 11: 803-816.

Malin 20080413 – Analysis of Eukaryotic Gene Structure Evolution

Malin 20080413

:: DESCRIPTION

Malin is a software package for the analysis of eukaryotic gene structure evolution. It provides a graphical user interface for various tasks commonly used to infer the evolution of exon-intron structure in protein-coding orthologs.

::DEVELOPER

Miklós Csűrös.

:: SCREENSHOTS

Malin

:: REQUIREMENTS

  • MacOsX / Linux /Windows
  • Java

:: DOWNLOAD

   Malin

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Jul 1;24(13):1538-9. doi: 10.1093/bioinformatics/btn226. Epub 2008 May 12.
Malin: maximum likelihood analysis of intron evolution in eukaryotes.
Csurös M.

Twinscan/N-SCAN 4.1.2 – Gene Structure Prediction

Twinscan/N-SCAN 4.1.2

:: DESCRIPTION

Twinscan/N-SCAN is a suite of software for gene-structure prediction. Twinscan is currently available for Mammals, Caenorhabditis (worm), Dicot plants, and Cryptococci. N-SCAN is available for human and Drosophila (fruitfly).

::DEVELOPER

The Brent Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

   Twinscan

:: MORE INFORMATION

Citation

Flicek P, Keibler E, Hu P, Korf I, Brent MR.
Leveraging the mouse genome for gene prediction in human: from whole-genome shotgun reads to a global synteny map.
Genome Res. 2003 Jan;13(1):46-54.

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