SSpred – Splice Site Prediction with Regulatory Elements and Dependencies

SSpred

:: DESCRIPTION

SSPred is a splice site prediction toolchain which incorporated a statistical model of splicing signals built based on the entropy density profile (EDP) method, weight array method (WAM), and kappa test, and a model of splicing regulatory elements developed by an unsupervised self-learning method to detect motifs associated with splicing regulatory elements.

::DEVELOPER

ZhuLab, Peking Uiniversity, Beijing

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 SSPred

:: MORE INFORMATION

dSSpred – Eukaryotic Donor Splice Site Prediction

dSSpred

:: DESCRIPTION

dSSpred is developed for the prediction of donor splice sites in eukaryotic species. It is based on all possible first order di-nucleotide dependencies that exist in the signal region at the exon-intron boundary.

::DEVELOPER

Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Nov 25;15(1):362.
A statistical approach for 5¿ splice site prediction using short sequence motifs and without encoding sequence data.
Meher P, Sahu T, Rao A, Wahi S.

NetUTR 1.0b – Web server for Prediction of Splice Site in 5′ UTRs

NetUTR 1.0b

:: DESCRIPTION

The NetUTR method presented here performs 2-3-fold better compared with NetGene2 and GenScan in 5′ UTRs (5′ untranslated regions).

::DEVELOPER

Eran Eden

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  Send inquiries by e-mail to software@cbs.dtu.dk.

:: MORE INFORMATION

Citation

Analysis and recognition of 5′ UTR intron splice sites in human pre-mRNA.
Eden E, Brunak S.
Nucleic Acids Res. 2004 Feb 11;32(3):1131-42.

ASP 0.3 – Accurate Splice Site Detection

ASP 0.3

:: DESCRIPTION

ASP is a program to predict accurate splice sites on genomic sequences of several organisms

::DEVELOPER

Rätsch Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ASP

:: MORE INFORMATION

Citation

Accurate splice site prediction using support vector machines.
Sonnenburg S, Schweikert G, Philips P, Behr J, Rätsch G.
BMC Bioinformatics. 2007;8 Suppl 10:S7.

 

PASSion 1.2.1 – Pattern Growth algorithm based Pileline for Splice Site Detection in Paired-end RNA-Seq data

PASSion 1.2.1

:: DESCRIPTION

PASSion uses the mapped read in a pair as anchor and then uses a high resolution algorithm, pattern growth, to remap the proximal and distal fragments of the unmapped read to a local region of the reference indicated by the mate. It is capable of identifying both known and novel canonical and non-canonical junctions with SNP or sequencing error tolerance.

::DEVELOPER

Yanju Zhang (Leiden University Medical Center, The Netherlands): y.zhang AT lumc.nl

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PASSion

:: MORE INFORMATION

Citation:

PASSion: A Pattern Growth Algorithm Based Pipeline for Splice Junction Detection in Paired-end RNA-Seq Data
Yanju Zhang; Eric-Wubbo Lameijer; Peter A.C. ‘t Hoen; Zemin Ning; P. Eline Slagboom; Kai Ye
Bioinformatics 2012; doi: 10.1093/bioinformatics/btr712

SpliceMachine – Splice Site Prediction Tool

SpliceMachine

:: DESCRIPTION

SpliceMachine is a splice site prediction tool that

  • shows state-of-the-art prediction performance on Arabidopsis thaliana and human sequences,
  • performs a computationally fast annotation and
  • can be trained by the user on its own data.

:: DEVELOPER

Bioinformatics & Systems Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SpliceMachine

:: MORE INFORMATION

Citation:

Degroeve, S., Saeys, Y., De Baets, B., Rouzé, P., Van de Peer, Y. (2005)
Predicting splice sites from high-dimensional local context representations.
Bioinformatics 21, 1332-8.

NetGene2 2.42 – Intron Splice Sites in Human, C. Elegans & A. Thaliana DNA

NetGene2 2.42

:: DESCRIPTION

NetGene2 is a service producing neural network predictions of splice sites in human, C. elegans and A. thaliana DNA.

::DEVELOPER

CBS (Center for Biological Sequence Analysis),  Technical University of Denmark

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

NetGene2 Source Code

:: MORE INFORMATION

Citation

S.M. Hebsgaard, P.G. Korning, N. Tolstrup, J. Engelbrecht, P. Rouze, S. Brunak
Splice site prediction in Arabidopsis thaliana DNA by combining local and global sequence information
Nucleic Acids Research, 1996, Vol. 24, No. 17, 3439-3452.

Brunak, S., Engelbrecht, J., and Knudsen, S.
Prediction of Human mRNA Donor and Acceptor Sites from the DNA Sequence
Journal of Molecular Biology, 1991, 220, 49-65.

GeneSplicer – Detecting Splice Sites in Eukaryotic Genomic DNA

GeneSplicer

:: DESCRIPTION

GeneSplicer is a fast, flexible system for detecting splice sites in the genomic DNA of various eukaryotes. The system has been trained and tested successfully on Plasmodium falciparum (malaria), Arabidopsis thaliana, human, Drosophila, and rice . Training data sets for human and Arabidopsis thaliana are included.

::DEVELOPER

the Center for Bioinformatics and Computational Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

GeneSplicer

:: MORE INFORMATION

The GeneSplicer software is OSI Certified Open Source Software.

Citation:

Pertea , X. Lin , S. L. Salzberg . GeneSplicer : a new computational method for splice site prediction . Nucleic Acids Res . 2001 Mar 1;29(5):1185-90 .