http://bioinformatics.ca/links_directory/tag/artificial-intelligencehttp://bioinformatics.ca/links_directory/tag/artificial-intelligence/feed en http://bioinfo3.noble.org/AtSubP/A highly accurate subcellular localization prediction tool for annotating the Arabidopsis thaliana proteome.13451Thu, 16 May 2013 22:40:34 -0400 http://www.imtech.res.in/raghava/rslpred/A subcellular localization prediction tool specifically developed for Rice (Oryza sativa) based on machine learning techniques.13450Tue, 14 May 2013 20:00:07 -0400 http://www.predictprotein.org/service for protein structure prediction, protein sequence analysis, protein function prediction, protein sequence alignments, bioinformatics13285Sat, 18 May 2013 02:20:37 -0400 http://www.imtech.res.in/raghava/ctlpredCTLPred is a direct method for prediction of CTL epitopes crucial in subunit vaccine design.In direct methods the information or patterns of T cell epitopes instead of MHC binders were used for the development of methods.12906Fri, 17 May 2013 11:20:17 -0400 http://www.nactem.ac.uk/deca_details/start.cgiDECA is a species disambiguation system for biological named entities. The system will identify protein entities and disambiguate them according to species, by assigning NCBI Taxonomy organism IDs. 12624Sat, 18 May 2013 04:50:24 -0400 http://www.nactem.ac.uk/acela/The ACELA (ACcElerated Annotation) tool aims to reduce the human effort required to produce a gold standard corpus of named entity (NE) annotations. 12442Sat, 18 May 2013 14:10:09 -0400 http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:PredUsPredUs is a web server for the prediction of protein-protein interfaces. The method predicts protein-protein interfaces of a given monomeric query protein using its close and remote structural neighbors.12114Fri, 10 May 2013 06:30:27 -0400 http://www.bioinformatics.sussex.ac.uk/PIRANHAThe PiRaNhA web server predicts the location of RNA binding residues in protein sequences using a support vector machine. Up to 10 protein sequences may be submitted.10676Tue, 14 May 2013 03:20:27 -0400 http://meme.nbcr.net/meme/intro.htmlThe MEME Suite web server is a unified portal for discovery and analysis of sequence motifs (e.g. DNA binding sites, protein interaction domains). Motifs with/without gaps may be discovered, searched for in DNA and protein databases, compared to other motifs and analyzed for putative function by association with gene ontology terms. MEME is a tool designed for discovering and searching for DNA motifs such as transcription factor binding sites (TFBS) or protein domains.10615Sat, 18 May 2013 04:10:26 -0400 http://www.mgene.org/webmGene.web is a web server for the genome wide prediction of protein coding genes from eukaryotic DNA sequences based on pre-computed models of gene structures. Users may also compute their own model using their own data.10587Fri, 17 May 2013 21:00:11 -0400 http://www.mitchell-lab.org/kfcThe KFC Server is a web-based implementation of the Knowledge-based FADE and Contacts (KFC) model. KFC predicts the subset of residues responsible for the majority of a protein interface's binding free energy. Users input protein-protein or protein-DNA information for visualization of binding hot spots within the protein structure.10469Thu, 16 May 2013 22:00:21 -0400 http://cbm.bio.uniroma2.it/SH3-Hunter/SH3-Hunter identifies putative SH3 domain interaction sites on protein sequences.10418Sat, 18 May 2013 09:30:22 -0400 http://bindr.gdcb.iastate.edu/RNABindR/RNABindR is a server for analyzing and predicting RNA binding sites in proteins.10405Fri, 17 May 2013 23:40:38 -0400 http://www.genome.jp/kegg/kaas/KAAS (KEGG Automatic Annotation Server) is a tool for ortholog assignment and pathway mapping. KAAS provides functional annotation of genes by BLAST comparisons against the manually curated KEGG GENES database. The result contains KO (KEGG Orthology) assignments and automatically generated KEGG pathways.10360Sat, 11 May 2013 10:00:31 -0400 http://www.bioinf.seu.edu.cn/Recombination/rf_dymhc.htmRF_DYMHC (Random Forest-Based System for Detecting Yeast Meiotic Recombination Hotspots and Coldspots) predicts recombination hot/cold spots in the yeast genome.10338Fri, 17 May 2013 04:40:11 -0400 http://phobius.sbc.su.se/Phobius is a combined transmembrane topology and signal peptide predictor. The server also allows for constrained and homology-enriched predictions.10337Wed, 15 May 2013 01:30:31 -0400 http://pipe.scs.fsu.edu/PI2PE (Protein Interface/Interior Prediction Engine) consists of three predictors (WESA, cons-PPISP, and DISPLAR) for predicting solvent accessibility and interface residues from the structure of a protein-binding or DNA-binding protein.10333Fri, 17 May 2013 05:00:22 -0400 http://www-abi.informatik.uni-tuebingen.de/Services/SVMHC/SVMHC is a server for prediction of MHC class I and class II binding peptides. SVMHC can be used to find likely binders in a protein sequence and to investigate the effects of single nucleotide polymorphisms on MHC-peptide binding.10294Sat, 18 May 2013 08:10:08 -0400 http://bioinformatics.ksu.edu/bindn/BindN takes an amino acid sequence as input and predicts potential DNA or RNA-binding residues using support vector machines (SVMs).10279Sat, 18 May 2013 09:50:34 -0400 http://bioinformatics.univ-reunion.fr/PBE/Protein Blocks Expert (PBE) uses a structural alphabet of short structural motifs to compare protein structures. PBE uses as its structural alphabet a set of protein blocks derived from structurally aligned homologous proteins present in the PALI Database.10266Fri, 17 May 2013 22:10:28 -0400 http://www.bioinfo.tsinghua.edu.cn/%7Etigerchen/memo.htmlMethylation Modification Prediction Server (MeMo) is a server that predicts arginine and lysine sites that undergo methylation using a support vector machine (SVM).10255Mon, 13 May 2013 13:00:17 -0400 http://pongo.biocomp.unibo.it/PONGO allows users to compare topology predictions of membrane proteins made by four different predictors (MEMSAT, TMHMM, ENSEMBLE, and PRODIV). It also displays a signal peptide prediction determined with SPEP.10238Thu, 16 May 2013 03:00:46 -0400 https://www2.informatik.uni-halle.de:8443/VOMBAT/faces/pages/choose.jspVOMBAT predicts transcription factor binding sites (TFBS) and other motifs in sequence data based on Variable Order Markov models and variable order BAyesian Trees.10241Fri, 17 May 2013 14:50:12 -0400 http://kobas.cbi.pku.edu.cnKEGG Orthology-Based Annotation System (KOBAS) annotates sequences with KEGG Orthology terms and identifies the frequently occurring (or significantly enriched) pathways among the queried sequences compared against a background distribution. 5 pathway databases are used (KEGG Pathway, PID, BioCyc, Reactome, Panther) and 5 human databases (OMIM, KEGG Disease, FunDO, GAD, NHGRI GWAS).10231Sat, 18 May 2013 06:50:29 -0400 http://www.geno2pheno.org/cgi-bin/geno2pheno.plGeno2pheno takes as input an HIV-1 pol-gene DNA sequence and estimates phenotypic drug resistance to 17 antiretroviral drugs.10182Sat, 18 May 2013 14:30:30 -0400 http://distill.ucd.ie/spritz/Spritz is a tool for the prediction of disordered regions of proteins.10161Sat, 18 May 2013 09:50:10 -0400 http://cluster.physics.iisc.ernet.in/ssep/options.htmlSecondary Structural Elements of Proteins (SSEP) provides access to information about secondary structural elements present in non-redundant sets of proteins from the PDB.10134Tue, 14 May 2013 11:40:20 -0400 http://www.nematodes.org/nembase4/NEMBASE is a resource for nematode transcriptome analysis, and a research tool for nematode biology, drug discovery and vaccine design. 10082Tue, 14 May 2013 10:50:18 -0400 http://www.genepath.org/genepath2GenePath is a tool for automated construction of genetic networks and proposal of genetic experiments from mutant data.10069Tue, 14 May 2013 21:20:12 -0400 http://www.imtech.res.in/raghava/pcleavage/Pcleavage is a tool that uses a support vector machine to predict immunoproteasome and constitutive proteasome cleavage sites in antigenic sequences.10059Thu, 16 May 2013 20:20:31 -0400 http://griffin.cbrc.jp/GRIFFIN (G-protein-Receptor Interacting Feature Finding INstrument) uses a support vector machine and hidden markov model to predict G-protein coupled receptors (GPCRs) and G-protein coupling selectivity.10052Thu, 16 May 2013 22:00:34 -0400 http://www.imtech.res.in/raghava/gpcrsclass/GPCRsclass is a tool for predicting amine-binding receptors based on a protein sequence provided by the user.10045Sun, 12 May 2013 07:50:15 -0400 http://gpcr2.biocomp.unibo.it/cgi/predictors/I-Mutant2.0/I-Mutant2.0.cgiI-Mutant2.0 is a tool that can predict the effect of a single point mutation on protein stability from protein sequences or protein structures.9970Wed, 15 May 2013 08:20:31 -0400 http://snpanalyzer.uthsc.edu/nsSNPAnalyzer is a tool to predict whether a nonsynonymous single nucleotide polymorphism (nsSNP) is phenotypically neutral or disease associated.9952Tue, 14 May 2013 07:50:17 -0400 http://cubic.bioc.columbia.edu/services/nlprot/index.htmlNLProt is a tool for finding protein names in natural language text. This data-mining method is a useful approach for extracting protein UniprotIDs from research articles for the construction of custom datasets and/or databases.9877Tue, 14 May 2013 02:50:25 -0400 http://www.imtech.res.in/raghava/gpcrpred/GPCRpred is a tool that uses a support vector machine based method to make GPCR family and subfamily predictions for a user-supplied query sequence.9839Sat, 18 May 2013 06:10:29 -0400 http://www.imtech.res.in/raghava/eslpred/ESLpred is a tool for predicting subcellular localization of proteins using support vector machines. The predictions are based on dipeptide and amino acid composition, and physico-chemical properties.9842Mon, 13 May 2013 22:50:30 -0400 http://bioinformatics.upmc.edu/GE2/GEDA.htmlThe Gene Expression Data Analyzer (GEDA) is a tool for discovering differential gene expression in a subset of patients. It is tailored to cancer-related microarray studies and offers extensive options for visualization, classification and normalization.9764Thu, 16 May 2013 14:00:10 -0400 http://www.cbs.dtu.dk/services/NetGene2/The NetGene2 server is a service producing neural network predictions of splice sites in human, C. elegans and A. thaliana DNA.9676Fri, 17 May 2013 17:30:32 -0400 http://www.expasy.ch/swissmod/SWISS-MODEL.htmlAutomated protein modelling server.9486Sun, 12 May 2013 13:40:24 -0400 http://casp.rnet.missouri.edu/domac.htmlDOMAC is an accurate, protein domain prediction server that integrates homology modeling, domain parsing, and ab initio methods together.9425Thu, 16 May 2013 13:41:01 -0400 http://disulfind.dsi.unifi.it/DISULFIND is a server for predicting the disulfide bonding state of cysteines and their disulfide connectivity given a protein sequence.9419Sat, 18 May 2013 14:30:35 -0400 http://bioinformatics.bc.edu/clotelab/DiANNA/DiANNA (DiAminoacid Neural Network Application) a tool that predicts cysteine states of a protein. It can predict whether a particular cysteine is reduced, is forming a disulfide bond, or is bound to a metallic ligand.9410Thu, 16 May 2013 19:00:24 -0400 http://www.fatigo.org/FatiGOplus is a tool for the functional profiling of genome-scale experiments oriented to the interpretation of microarray experiments. As part of the Babelomics suite, FatiGOplus finds differential distributions of biological terms (GO, KEGG pathways, Interpro motifs, Transfac motifs, CisRed motifs, etc.) between two groups of genes.9307Sat, 18 May 2013 01:20:21 -0400 http://www.imtech.res.in/raghava/bhairpred/BhairPred is a tool for predicting beta-hairpins in protein sequences using a support vector machine.9266Fri, 10 May 2013 20:50:16 -0400 http://phylogenomics.berkeley.edu/The Berkeley Phylogenomics Group provides a series of web servers for phylogenomic analysis: classification of sequences to pre-computed families and subfamilies using the PhyloFacts Phylogenomic Encyclopedia, FlowerPower clustering of proteins sharing the same domain architecture, MUSCLE multiple sequence alignment, SATCHMO simultaneous alignment and tree construction, and SCI-PHY subfamily identification.9265Sat, 18 May 2013 03:00:29 -0400 http://bioinf.uni-greifswald.de/augustusAUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface, or downloaded and run locally.9254Fri, 17 May 2013 00:00:32 -0400 http://www.imtech.res.in/raghava/algpred/AlgPred predicts allergenic proteins and maps IgE epitopes on allergenic proteins using several different approaches.9221Fri, 17 May 2013 12:40:23 -0400