GeneAnnot 2.2 – Microarray Gene Annotation

GeneAnnot 2.2

:: DESCRIPTION

The GeneAnnot system explores the many-to-many relationship between probe-sets and genes, by directly comparing the individual probe sequences with publicly available cDNAs and predicted genes from GenBank, RefSeq and Ensembl. The transcript sequences are further identified as GeneCards genes using the GeneLoc system which merges LocusLink and Ensembl gene indices on the basis of their genomic position.

::DEVELOPER

GeneAnnot team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2007 Nov 15;8:446.
Novel definition files for human GeneChips based on GeneAnnot.
Ferrari F1, Bortoluzzi S, Coppe A, Sirota A, Safran M, Shmoish M, Ferrari S, Lancet D, Danieli GA, Bicciato S.

Bioinformatics. 2004 Jun 12;20(9):1457-8. Epub 2004 Feb 12.
GeneAnnot: comprehensive two-way linking between oligonucleotide array probesets and GeneCards genes.
Chalifa-Caspi V, Yanai I, Ophir R, Rosen N, Shmoish M, Benjamin-Rodrig H, Shklar M, Stein TI, Shmueli O, Safran M, Lancet D.

GARNET – Gene Annotation Relationship Network tools

GARNET

:: DESCRIPTION

GARNET is an integrative platform for diverse types of gene set analysis with annotation network navigation. It includes tools for statistical analysis, visualization of annotation relationships, retrieval of genes from annotation database, and set operation for gene sets.

::DEVELOPER

Ewha Research Center for Systems Biology (ERCSB)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

GARNET–gene set analysis with exploration of annotation relations.
Rho K, Kim B, Jang Y, Lee S, Bae T, Seo J, Seo C, Lee J, Kang H, Yu U, Kim S, Lee S, Kim WK.
BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S25. doi: 10.1186/1471-2105-12-S1-S25.

Gene characterization index – Assessing the Depth of Gene Annotation

Gene characterization index

:: DESCRIPTION

Gene Characterization Index is a bioinformatics method for scoring the extent to which a protein-encoding gene is functionally described.

::DEVELOPER

The Wasserman Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PLoS One. 2008 Jan 23;3(1):e1440. doi: 10.1371/journal.pone.0001440.
Gene characterization index: assessing the depth of gene annotation.
Kemmer D, Podowski RM, Yusuf D, Brumm J, Cheung W, Wahlestedt C, Lenhard B, Wasserman WW.

INSEGT 1.0 – Analyse Alignments of RNA-Seq reads using Gene Annotations

INSEGT 1.0

:: DESCRIPTION

INSEGT is a tool to analyse alignments of RNA-Seq reads (single-end or paired-end) by using gene annotations. It can measure exon, transcript and gene expression levels of given annotations. If read alignments span more than one exon, INSEGT can also compute possible exon combinations (tuple) and their expression levels. According to requirements it computes maximal tuple or tuple with a certain length. For paired-end reads INSEGT builds also tuple, whose exons are connected by matepairs. Briefly it searches the intervals of the read alignments in the intervals of the given annotations. It counts the mapped reads for each annotation and its parent annotation and stores the mapped annotations for each read.

::DEVELOPER

David Weese , Sabrina Krakau.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows

:: DOWNLOAD

 INSEGT

:: MORE INFORMATION

JIGSAW 3.2.10 – Automated Gene Annotation System

JIGSAW 3.2.10

:: DESCRIPTION

JIGSAW is a program designed to use the output from gene finders, splice site prediction programs and sequence alignments to predict gene models. The program provides an automated way to take advantage of the many succsessful methods for computational gene prediction and can provide substantial improvements in accuracy over an individual gene prediction program.

::DEVELOPER

Jonathan E. Allen at the Center for Bioinformatics and Computational Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

JIGSAW

:: MORE INFORMATION

The JIGSAW software is OSI Certified Open Source Software.

Citation:

J.E. Allen, W.H. Majoros, M. Pertea, and S.L. Salzberg.  JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions.  Genome Biology 2007, 7(Suppl):S9.