:: DESCRIPTION
ExUTR is a practical and powerful tool that enables rapid genome-wide 3′-UTR prediction from massive RNA-Seq data
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Huang Z, Teeling EC.
ExUTR: a novel pipeline for large-scale prediction of 3′-UTR sequences from NGS data.
BMC Genomics. 2017 Nov 6;18(1):847. doi: 10.1186/s12864-017-4241-1. PMID: 29110697; PMCID: PMC5674806.
:: DESCRIPTION
SUMOsp based on a manually curated dataset, integrating the results of two methods, GPS and MotifX, which were originally designed for phosphorylation site prediction. SUMOsp offers at least as good prediction performance as the only available method, SUMOplot, on a very large test set. We expect that the prediction results of SUMOsp combined with experimental verifications will propel our understanding of sumoylation mechanisms to a new level.
GPS-SUMO is a tool for the prediction of sumoylation sites and SUMO-interaction motifs.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
GPS-SUMO: a tool for the prediction of sumoylation sites and SUMO-interaction motifs.
Zhao Q, Xie Y, Zheng Y, Jiang S, Liu W, Mu W, Liu Z, Zhao Y, Xue Y, Ren J.
Nucleic Acids Res. 2014 May 31. pii: gku383
Systematic study of protein sumoylation: Development of a site-specific predictor of SUMOsp 2.0.
Jian Ren, Xinjiao Gao, Changjiang Jin, Mei Zhu, Xiwei Wang, Andrew Shaw, Longping Wen, Xuebiao Yao and Yu Xue.
Proteomics.2009; 9:3409-3412
:: DESCRIPTION
HEA-PSP is a hybrid evolutionary search framework with various crossover implementations for Ab-initio protein structre prediction
::DEVELOPER
Computational Biology lab, George Mason University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Brian Olson, Kenneth A. De Jong, and Amarda Shehu.
Off-Lattice Protein Structure Prediction with Homologous Crossover.
GECCO 2013, pages 287-294, Amsterdam,
:: DESCRIPTION
SEPPA (Spatial Epitope Prediction of Protein Antigens) is spatial epitope prediction for protein antigens, particularly for N-linked glycoproteins
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DESCRIPTION
BETAWARE is a software package designed for the analysis of trans-membrane beta-barrel proteins.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2013 Feb 15;29(4):504-5. doi: 10.1093/bioinformatics/bts728. Epub 2013 Jan 6.
BETAWARE: a machine-learning tool to detect and predict transmembrane beta-barrel proteins in prokaryotes.
Savojardo C, Fariselli P, Casadio R.
:: DESCRIPTION
RPISeq is a family of classifiers for predicting RNA-protein interactions using only sequence information.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation:
BMC Bioinformatics. 2011 Dec 22;12:489. doi: 10.1186/1471-2105-12-489.
Predicting RNA-protein interactions using only sequence information.
Muppirala UK1, Honavar VG, Dobbs D.
:: DESCRIPTION
miR-AT! is a computational tool for the identification of all transcripts that are targets of a list of input miRNAs.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation:
Dombkowski A.A., Sultana, Z., Craig, D.B., Jamil, H.,
In silico analysis of combinatorial microRNA activity reveals target genes and pathways associated with breast cancer metastasis.
Cancer Informatics, 2011;10:13-29
:: DESCRIPTION
Targetprofiler is a novel miRNA target prediction tool that utilizes a probabilistic learning algorithm in the form of a hidden Markov model trained on experimentally verified miRNA targets.
::DEVELOPER
Ioannis Iliopoulos’ Bioinformatics & Computational Biology Lab
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
RNA Biol. 2012 Sep;9(9):1196-207. doi: 10.4161/rna.21725. Epub 2012 Sep 1.
A new microRNA target prediction tool identifies a novel interaction of a putative miRNA with CCND2.
Oulas A1, Karathanasis N, Louloupi A, Iliopoulos I, Kalantidis K, Poirazi P.
:: DESCRIPTION
LOGICOIL, the first algorithm to address the problem of predicting multiple coiled-coil oligomeric states from protein-sequence information alone.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
“LOGICOIL: Multi-state classification of coiled-coil oligomeric state.”
T. L. Vincent, P.J. Green and D. N. Woolfson.
Bioinformatics (2013) 29 (1): 69-76.
:: DESCRIPTION
PepFly constructs a dataset for easy importation into the Weka machine learning toolkit from MS datasets to predict the flyability of peptides.
:: DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2007 Nov 1;8 Suppl 7:S23.
Prediction of peptides observable by mass spectrometry applied at the experimental set level.
Sanders WS, Bridges SM, McCarthy FM, Nanduri B, Burgess SC.