Luciphor2 – PTM-site localization on MS/MS data

Luciphor2

:: DESCRIPTION

Luciphor2 is a site localization tool for generic post-translational modifications (PTMs) using tandem mass spectrometry data.

::DEVELOPER

Proteomics & Integrative Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

 Luciphor2

:: MORE INFORMATION

Citation:

Bioinformatics. 2015 Apr 1;31(7):1141-3. doi: 10.1093/bioinformatics/btu788. Epub 2014 Nov 25.
LuciPHOr2: site localization of generic post-translational modifications from tandem mass spectrometry data.
Fermin D, Avtonomov D, Choi H, Nesvizhskii AI

EnTrans-Chlo – Transductive Learning for Protein Subchloroplast Localization

EnTrans-Chlo

:: DESCRIPTION

EnTrans-Chlo is an efficient multi-label predictor which is based on a transductive model for predicting single- and multi-location chloroplast proteins. EnTrans-Chlo represents using a TRANSductive-learning based algorithm to exploit ENsemble features of both sequence-based and evolutionary-based information to predictor protein subCHLOroplast localization.

::DEVELOPER

Dr. Man-Wai Mak

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

IEEE/ACM Trans Comput Biol Bioinform. 2016 Feb 8.
Transductive Learning for Multi-Label Protein Subchloroplast Localization Prediction.
Wan S, Mak MW, Kung SY.

MiRdup 1.4 – Prediction of the Localization of microRNAs within their pre-miRNA

MiRdup 1.4

:: DESCRIPTION

miRdup is a computational predictor for the identification of the most likely miRNA location within a given pre-miRNA or the validation of a candidate miRNA.

::DEVELOPER

Mickael Leclercq (mickael.leclercq@mail.mcgill.ca)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 MiRdup

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Aug;41(15):7200-11. doi: 10.1093/nar/gkt466. Epub 2013 Jun 8.
Computational prediction of the localization of microRNAs within their pre-miRNA.
Leclercq M1, Diallo AB, Blanchette M.

ProCon 1.1 – Localization & Visualization of Protein Conservation

ProCon 1.1

:: DESCRIPTION

ProCon is tool for locating and visualization of evolutionary conservation in protein sequences. The method can identify three types of conservation: identity (type I), physicochemical similarity (II), and covariant conservation (III). The conservative sites of type I and II are located with entropy calculation and the third type is identified by calculation of mutual information. The interacting networks formed by covariant pairs can also be identified. All the three types of conservation can be visualized in a representative protein structure. The tool performs exhaustive analysis results of which can be used e.g. for identifying different types of conserved residues, studying protein-protein interactions, explaining consequences of disease-causing mutations and mutant design for protein engineering.

::DEVELOPER

ProCon Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac
  • Java

:: DOWNLOAD

 ProCon

:: MORE INFORMATION

MultiP-SChlo – Multi-Label Protein Subchloroplast Localization Prediction

MultiP-SChlo

:: DESCRIPTION

MultiP-SChlo is a web server of multi-label protein subchloroplast localization prediction with Chou’s pseudo amino acid composition and a novel multi-label classifier

::DEVELOPER

MultiP-SChlo team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

MultiP-SChlo: multi-label protein subchloroplast localization prediction with Chou’s pseudo amino acid composition and a novel multi-label classifier.
Wang X, Zhang W, Zhang Q, Li GZ.
Bioinformatics. 2015 Apr 20. pii: btv212.

SubNucPred – Web-server for Prediction of Sub-nuclear Localization of Proteins

SubNucPred

:: DESCRIPTION

SubNucPred is a combined method of two different prediction approaches which predicts 10 different sub-nuclear locations namely: centromere, chromosome, nucleolus, nuclear envelope, nuclear speckles, telomere, nucleoplasm, nuclear matrix, PML body and nuclear pore complex.

::DEVELOPER

Dr. Manish Kumar

:: SCREENSHOTS

N/a

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SubNucPred

:: MORE INFORMATION

Citation

PLoS One. 2014 Jun 4;9(6):e98345. doi: 10.1371/journal.pone.0098345. eCollection 2014.
Protein sub-nuclear localization prediction using SVM and Pfam domain information.
Kumar R, Jain S, Kumari B, Kumar M

PSI-predictor – Plant Subcellular Localization Prediction

PSI-predictor

:: DESCRIPTION

PSI-predictor (Plant Subcellular localization Integrative predictor) is currently the most comprehensive and integrative subcellular location predictor for plants. Based on the wisdom of group-voting and artificial neural network, PSI integrated prediction results from 11 individual predictors to give accurate results on cytosol (cytos), endoplasmic reticulum (ER), extracellular (extra), golgi apparatus (golgi), membrane (membr), mitochondria (mito), nuclear (nucl), peroxisome (pero), plastid (plast) and vacuole (vacu). The community outperformed each individual predictor both on every subcellular location (≥0.8) and overall, with an AUROC~0.932.

::DEVELOPER

Ming Chen’s Bioinformatics Group, Zhejiang University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Lili Liu, Zijun Zhang, Qian Mei, Ming Chen (2013)
PSI: A comprehensive and integrative approach for accurate plant subcellular localization prediction,
PLoS One, DOI:10.1371/journal.pone.0075826

LOCO-LD – LOcalization COrrected for Linkage Disequilibrium

LOCO-LD

:: DESCRIPTION

LOCO-LD is a method for the geographic localization of individuals. It takes as input genotype data and generates, for each individual, an estimate for their geographic coordinates of origin.

::DEVELOPER

Bogdan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • C Compiler
  • Matlab

:: DOWNLOAD

 LOCO-LD

:: MORE INFORMATION

Citation:

Enhanced Localization of Genetic Samples through Linkage-Disequilibrium Correction
Yael Baran, Inés Quintela, ángel Carracedo, Bogdan Pasaniuc, Eran Halperin
The American Journal of Human Genetics – 6 June 2013 (Vol. 92, Issue 6, pp. 882-894)

MemPype – Pipeline for Predicting the Topology and the Localization of Membrane Proteins

MemPype

:: DESCRIPTION

MemPype is a Python-based pipeline that integrates several tools the prediction of topology and subcellular localization of Eukaryotic membrane proteins.

::DEVELOPER

Bologna Biocomputing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 No. Only Web Service

:: MORE INFORMATION

Citation

Pierleoni A, Indio V, Savojardo C, Fariselli P, Martelli PL, Casadio R.
MemPype: a pipeline for the annotation of eukaryotic membrane proteins.
Nucl. Acids Res. (2011) 39 (suppl 2): W375-W380.

CopyMap 0.813 – Localization of Copy Number Variation

CopyMap 0.813

:: DESCRIPTION

CopyMap is a hidden Markov algorithm to infer copy number variation from a sample of hybridization intensities. The program combines the information across individuals by estimating a transition matrix between every pair of markers using a Baum‐Welch algorithm. The algorithm consists of two steps, the first step estimates the underlying parameters, the second step estimates carrier status in each individual based on the estimated parameters

::DEVELOPER

Sebastian Zöllner @ the Center for Statistical Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • C Complier

:: DOWNLOAD

  CopyMap

:: MORE INFORMATION

Citation

Sebastian Zöllner
CopyMap: localization and calling of copy number variation by joint analysis of hybridization data from multiple individuals.
Bioinformatics (Oxford, England) 2010;26(21):2776-7.