SplicingTypesAnno 1.0.2 – Annotation tool for alternative Splicing Types by RNA-Seq data

SplicingTypesAnno 1.0.2

:: DESCRIPTION

SplicingTypesAnno annotates four major splicing types by RNA-Seq data, including intron retention, exon skipping, alternative donor site, and alternative acceptor site. As a post-processing tool for alignment files, it annotates the alternative splicing types with details at the intron or exon level.

:: DEVELOPER

Dr. Xiaoyong Sun, Genomics and Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / WIndows

:: DOWNLOAD

SplicingTypesAnno

:: MORE INFORMATION

Citation

Comput Methods Programs Biomed. 2015 Feb 14. pii: S0169-2607(15)00028-0. doi: 10.1016/j.cmpb.2015.02.004. [Epub ahead of print]
SplicingTypesAnno: Annotating and quantifying alternative splicing events for RNA-Seq data.
Sun X, Zuo F, Ru Y, Guo J, Yan X, Sablok G

COUDES 1.0 – Prediction of Beta-turns and their Types

COUDES 1.0

:: DESCRIPTION

COUDES (Chercher Où Une Deviation Existe Sûrement.) is a tool for predicting beta-turns and their type in a protein or peptide sequence.

::DEVELOPER

the DSIMB bioinformatic group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

High accuracy prediction of beta-turns and their types using propensities and multiple alignments.
Fuchs PF, Alix AJ.
Proteins. 2005 Jun 1;59(4):828-39.

Mem-ADSVM – Multi-Label Membrane Protein Type Prediction

Mem-ADSVM

:: DESCRIPTION

Mem-ADSVM is a two-layer multi-label membrane-protein functional-type predictor, which can identify membrane proteins (Layer I) and their multi-functional types (Layer II).

::DEVELOPER

Dr. Man-Wai Mak

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Mem-ADSVM: A Two-Layer Multi-Label Predictor for Identifying Multi-Functional Types of Membrane Proteins.
Wan S, Mak MW, Kung SY.
J Theor Biol. 2016 Mar 18. pii: S0022-5193(16)00154-5. doi: 10.1016/j.jtbi.2016.03.013.

iMem-Seq – Predicting Membrane Proteins Types

iMem-Seq

:: DESCRIPTION

iMem-Seq is a multi-label classifier for identifying membrane proteins with single and multiple types via physical-chemical property matrix and grey-PSSM

::DEVELOPER

Xiao Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

J Membr Biol. 2015 Aug;248(4):745-52. doi: 10.1007/s00232-015-9787-8. Epub 2015 Mar 22.
iMem-Seq: A Multi-label Learning Classifier for Predicting Membrane Proteins Types.
Xiao X1, Zou HL, Lin WZ.

MemType-2L – Predicting Membrane Protein Types

MemType-2L

:: DESCRIPTION

MemType-2L is a 2-layer predictor for predicting membrane protein types, the first layer will predict whether the query sequence belongs to membrane proteins or not; and the second layer aims to predict exactly the membrane protein types when the output of the first layer is “membrane proteins”.

::DEVELOPER

Computational Systems Biology Group, Shanghai Jiao Tong University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

Biochem Biophys Res Commun. 2007 Aug 24;360(2):339-45. Epub 2007 Jun 15.
MemType-2L: a web server for predicting membrane proteins and their types by incorporating evolution information through Pse-PSSM.
Chou KC1, Shen HB.

Mem-mEN – Interpretable Membrane Protein Type Prediction

Mem-mEN

:: DESCRIPTION

Mem-mEN leverages a multi-label elastic net (EN) classifier, which can yield sparse and interpretable solutions for large-scale prediction of membrane proteins with single- and multi-label functional types.

::DEVELOPER

Dr. Man-Wai Mak

:: SCREENSHOTS

N/A

::REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

IEEE/ACM Trans Comput Biol Bioinform. 2015 Aug 28.
Mem-mEN: Predicting Multi-Functional Types of Membrane Proteins by Interpretable Elastic Nets.
Wan S, Mak MW, Kung SY.