AlignExIn 20130624 – Alignment Exon Intron Structure

AlignExIn 20130624

:: DESCRIPTION

AlignExIn ( Align Exon Intron) is a handy and useful utility built in order to display the alignment of exons. The program displays the exon painted in red and the alignments painted in blue by default, but it is possible to change the colors.All you have to do is select the input files (fasta and exon) and the program will do the rest.

::DEVELOPER

Institute of Bioinformatics WWU Muenster

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows / MacOsX
Java

:: DOWNLOAD

alignexin

:: MORE INFORMATION

FirstEF – Human First Exon Finder

FirstEF

:: DESCRIPTION

FirstEF (First Exon Finder) is a 5′ terminal exon and promoter prediction program. It consists of different discriminant functions structured as a decision tree. The probabilistic models are optimized to find potential first donor sites and CpG-related and non-CpG-related promoter regions based on discriminant analysis. For every potential first donor site (GT) and an upstream promoter region, FirstEF decides whether or not the intermediate region can be a potential first exon, based on a set of quadratic discriminant functions.

::DEVELOPER

Michael Zhang Computational Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Computational identification of promoters and first exons in the human genome.
Davuluri RV, Grosse I, Zhang MQ.
Nat Genet. 2001 Dec;29(4):412-7. Erratum in: Nat Genet 2002 Nov;32(3):459.

Noncoder – Exon Array-based Detection of Long non-coding RNA

Noncoder

:: DESCRIPTION

noncoder is a web server for analyzing Affymetrix GeneChip Exon 1.0 ST arrays (exon arrays) for expression changes of long non-coding RNAs (lncRNAs).

::DEVELOPER

Noncoder team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2013 Jan 7;41(1):e20. doi: 10.1093/nar/gks877. Epub 2012 Sep 24.
Noncoder: a web interface for exon array-based detection of long non-coding RNAs.
Gellert P1, Ponomareva Y, Braun T, Uchida S.

ExonFinder 2.0 – Extract novel Cassette Exons/Retained-introns

ExonFinder 2.0

:: DESCRIPTION

ExonFinder provides a pipeline to extract novel cassette exons and novel retained-introns from the results of mapping cross-species ESTs against a target genome via blat.

::DEVELOPER

ExonFinder team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

ExonFinder

:: MORE INFORMATION

Citation

BMC Plant Biol. 2015 Feb 5;15(1):39.
Comparative genomics of grass EST libraries reveals previously uncharacterized splicing events in crop plants.
Chuang TJ, Yang MY, Lin CC, Hsieh PH, Hung LY.

GESS 1.0 – Exon-skipping Scanner Detection program for RNA-seq data

GESS 1.0

:: DESCRIPTION

GESS (graph-based exon-skipping scanner) is a novel computational method for de novo detection of skipping event sites from raw RNA-seq reads without prior knowledge of gene annotations, as well as for determining the dominant isoform generated from such sites.

::DEVELOPER

Jin Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

GESS

:: MORE INFORMATION

Citation

Ye Z, Chen Z, Lan X, Hara S, Sunkel B, Huang TH, Elnitski L, Wang Q, Jin VX.
Computational analysis reveals a correlation of exon-skipping events with splicing, transcription and epigenetic factors.
Nucleic Acids Res. 2014 Mar 1;42(5):2856-69.

GeneLoc 4.8 – Exon-based Integration of Human Genome Maps

GeneLoc 4.8

:: DESCRIPTION

GeneLoc (Gene Location) presents an integrated map for each human chromosome, based on data integrated by the GeneLoc algorithm

::DEVELOPER

GeneLoc team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

Bioinformatics. 2003;19 Suppl 1:i222-4.
GeneLoc: exon-based integration of human genome maps.
Rosen N, Chalifa-Caspi V, Shmueli O, Adato A, Lapidot M, Stampnitzky J, Safran M, Lancet D.

PrimerZ 20171130 – Streamlined Primer design for Promoters, Exons and Human SNPs

PrimerZ 20171130

:: DESCRIPTION

PrimerZ is a web application dedicated primarily to primer design for genes and human SNPs.

::DEVELOPER

PrimerZ team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

PrimerZ: streamlined primer design for promoters, exons and human SNPs.
Tsai MF, Lin YJ, Cheng YC, Lee KH, Huang CC, Chen YT, Yao A.
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W63-5. Epub 2007 May 30.

ACEScan 1.0 – Prediction of Conserved Alternatively Spliced Exons from pairs of Conserved Mouse/Human Exons

ACEScan 1.0

:: DESCRIPTION

ACEScan is a webtool of identification and analysis of alternative splicing events conserved in human and mouse.

::DEVELOPER

Christopher Burge Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Yeo, G., Van Nostrand, E., Holste, D., Poggio, T. and Burge, C. B. (2005).
Identification and analysis of alternative splicing events conserved in human and mouse.
Proc. Natl. Acad. Sci. USA 102, 2850-2855

ESEfinder 3.0 – Exon Splicing Enhancer Finder

ESEfinder 3.0

:: DESCRIPTION

ESEfinder is a web-based resource that facilitates rapid analysis of exon sequences to identify putative ESEs responsive to the human SR proteins SF2/ASF, SC35, SRp40 and SRp55, and to predict whether exonic mutations disrupt such elements.

::DEVELOPER

ESEfinder team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Smith, P. J., Zhang, C., Wang, J. Chew, S. L., Zhang, M. Q. and Krainer, A. R. 2006.
An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancers.
Hum. Mol. Genet. 15(16): 2490-2508.

Cartegni L., Wang J., Zhu Z., Zhang M. Q., Krainer A. R.; 2003.
ESEfinder: a web resource to identify exonic splicing enhancers.
Nucleic Acid Research, 2003, 31(13): 3568-3571.

rMAPS 2.0.0 – RNA Map analysis and Plotting server for alternative Exon Regulation

rMAPS 2.0.0

:: DESCRIPTION

rMAPS (rna Map Analysis and Plotting Server) is a web server that systematically generates RNA-maps for the analysis of RNA-binding proteins (RBPs) binding sites which have position-dependent functions.

::DEVELOPER

rMAPS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

rMAPS: RNA map analysis and plotting server for alternative exon regulation.
Park JW, Jung S, Rouchka EC, Tseng YT, Xing Y.
Nucleic Acids Res. 2016 May 12. pii: gkw410.