Tag: alternative

SpliceSeq 2.1 – Investigate alternative mRNA Splicing in Next Generation mRNA Sequence data

SpliceSeq 2.1

:: DESCRIPTION

SpliceSeq provides a quick, easy method of investigating alternative mRNA splicing in next generation mRNA sequence data. The tool may be used on a single mRNA-Seq sample to identify genes with multiple spliceforms or on a pair of samples to identify differential splicing between the samples. Sequence reads are mapped to splice graphs that unambiguously quantify the inclusion level of each exon and splice junction. The graphs are then traversed to predict the protein isoforms that are likely to result from the observed exon and splice junction reads. UniProt annotations are mapped to each protein isoform to identify potential functional impacts of alternative splicing.

::DEVELOPER

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 SpliceSeq

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Sep 15;28(18):2385-7. Epub 2012 Jul 20.
SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts.
Ryan MC, Cleland J, Kim R, Wong WC, Weinstein JN.

nagnag 1.0.3 – Identifyng and Quantifying NAGNAG Alternative Splicing

nagnag 1.0.3

:: DESCRIPTION

nagnag is an R package for NAGNAG alternative splicing

:: DEVELOPER

Dr. Xiaoyong Sun, Genomics and Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows
  • R

:: DOWNLOAD

 nagnag

:: MORE INFORMATION

Citation

Biomed Res Int. 2014;2014:736798. doi: 10.1155/2014/736798. Epub 2014 Jun 5.
Computational evidence of NAGNAG alternative splicing in human large intergenic noncoding RNA.
Sun X, Lin SM, Yan X

nagnag: Identification and quantification of NAGNAG alternative splicing using RNA-Seq data.
Yan X, Sablok G, Feng G, Ma J, Zhao H, Sun X.
FEBS Lett. 2015 May 27. pii: S0014-5793(15)00423-8. doi: 10.1016/j.febslet.2015.05.029

CAMUR – Classifier with Alternative and MUltiple Rule-based models

CAMUR

:: DESCRIPTION

CAMUR is a new method and software package able to extract multiple, alternative, and equivalent classification models.

::DEVELOPER

DMB (Data Mining Big) Team

:: SCREENSHOTS

CAMUR

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • java

:: DOWNLOAD

 CAMUR

:: MORE INFORMATION

Citation

CAMUR: Knowledge extraction from RNA-seq cancer data through equivalent classification rules.
Cestarelli V, Fiscon G, Felici G, Bertolazzi P, Weitschek E.
Bioinformatics. 2015 Oct 30. pii: btv635.

ALTSCAN 1.0 – ALTernative Splicing SCANner

ALTSCAN 1.0

:: DESCRIPTION

ALTSCAN is an ab initial alternative splicing predictor whose primary purpose is to explore protein-coding structures as many as possible.

::DEVELOPER

Dr. Chaochun Wei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ALTSCAN

:: MORE INFORMATION

Citation

Hu, Z., Scott, H., Qin, G., Zheng, G, Chu, X., Xie, L., Adelson, D., Oftedal, B., Venugopal, P., Babic, M., Hahn, C., Zhang, B., Wang, X., Li, N., Wei, C.*,
Revealing missing human protein isoforms based on ab initio prediction, RNA-seq and proteomics
Scientific Reports, 2015, 5:10940.

MutualFold – Simultaneous Folding of Alternative RNA Structures with Mutual Constraints

MutualFold

:: DESCRIPTION

MutualFold is an application to next-generation sequencing based RNA structure probing.

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MutualFold

:: MORE INFORMATION

Citation:

J Comput Biol. 2014 Aug;21(8):609-21. doi: 10.1089/cmb.2013.0044. Epub 2014 Apr 1.
Simultaneous folding of alternative RNA structures with mutual constraints: an application to next-generation sequencing-based RNA structure probing.
Zhong C1, Zhang S.

ALEXA-Seq 1.17 – Alternative Expression Analysis by massively parallel RNA Sequencing

ALEXA-Seq 1.17

:: DESCRIPTION

ALEXA-Seq is a method for using massively parallel paired-end transcriptome sequencing for ‘alternative expression analysis’.

::DEVELOPER

ALEXA-Seq Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Virtual Machines

:: DOWNLOAD

 ALEXA-Seq

:: MORE INFORMATION

Citation:

Malachi Griffith, et al.
Alternative expression analysis by RNA sequencing.
Nature Methods. 2010 Oct;7(10):843-847.