:: DESCRIPTION
MemPype is a Python-based pipeline that integrates several tools the prediction of topology and subcellular localization of Eukaryotic membrane proteins.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: SCREENSHOTS
N/a
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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)
:: 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
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
HybridGO-Loc stands for mining Hybrid features on Gene Ontology (GO) for protein subcellular Localization prediction, meaning that this predictor extracts the feature of proteins from different perspectives of GO information (i.e. GO frequency occurrences and GO semantic similarity) and then processes the information by a multi-label multi-class SVM classifier with an adaptive decision scheme.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Wan S, Mak MW, Kung SY.
HybridGO-Loc: mining hybrid features on gene ontology for predicting subcellular localization of multi-location proteins.
PLoS One. 2014 Mar 19;9(3):e89545. doi: 10.1371/journal.pone.0089545. PMID: 24647341; PMCID: PMC3960097.
:: 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
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: 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.
:: DESCRIPTION
KnockoffZoom localizes causal variants precisely and provably controls the false discovery rate using artificial genotypes as negative controls.
KnockoffGWAS is a powerful and versatile statistical method for the analysis of genome-wide association data with population structure.
::DEVELOPER
the Sabatti Lab
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Sesia M, Katsevich E, Bates S, Candès E, Sabatti C.
Multi-resolution localization of causal variants across the genome.
Nat Commun. 2020 Feb 27;11(1):1093. doi: 10.1038/s41467-020-14791-2. Erratum in: Nat Commun. 2020 Apr 7;11(1):1799. PMID: 32107378; PMCID: PMC7046731.
:: 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
:: DOWNLOAD
:: 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
:: 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
Mathieu Blanchette’sComputational Genomics Lab
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: DOWNLOAD
:: 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
