http://bioinformatics.ca/links_directory/tag/statistical-modelshttp://bioinformatics.ca/links_directory/tag/statistical-models/feed en http://www.cs.toronto.edu/~hilal/rnacontext/RNAcontext: a new motif-finding method designed to elucidate RNA-binding protein (RBP) specific sequence and structural preferences with greater accuracy than existing approahces. 13404Thu, 23 May 2013 11:10:31 -0400 http://www.esat.kuleuven.be/endeavourENDEAVOUR is a computational approach to prioritize candidate genes for further study. Users input training genes already known to be involved in the process under study and the candidate genes to prioritize. The web server supports multiple species and integrates multiple genomic data to generate the final prioritization. ENDEAVOUR has been benchmarked in silico and experimentally validated leading to the discovery of novel disease genes in several genetic diseases.12956Thu, 23 May 2013 20:10:11 -0400 http://www.imtech.res.in/raghava/alphapred/The AlphaPred server predicts the alpha turn residues in the given protein sequence. The method is based on the neural network training on PSI-BLAST generated position specific matrices and PSIPRED predicted secondary structure.12899Thu, 23 May 2013 05:30:31 -0400 http://www.imtech.res.in/raghava/betatpred2/The aim of BetaTPred2 server is to predict ß turns in proteins from multiple alignment by using neural network from the given amino acid sequence. For ß turn prediction, it uses the position specific score matrices generated by PSI-BLAST and secondary structure predicted by PSIPRED.12897Thu, 23 May 2013 20:20:27 -0400 http://text0.mib.man.ac.uk/~sasaki/bootstrep/nemine.htmlRecognises gene and protein names in biomedical text.12439Thu, 23 May 2013 01:50:49 -0400 http://www.nactem.ac.uk/software/acromine_disambiguation/Given a biomedical text, Acromine Disambiguator correctly predicts expanded full forms of acronoyms appearing in the text. As acronyms appearing in biomedical texts are often ambiguous, such a disambiguation process is important to ensure the correct interpretation of the text. 12435Tue, 21 May 2013 19:10:16 -0400 http://www.nactem.ac.uk/software/acromine/Acromine is an tool that finds full forms of acronyms that appear in MEDLINE. 12434Wed, 22 May 2013 01:50:45 -0400 http://bioinfo.townsend.yale.edu/The filamentous fungal gene expression database (FFGED) is a user-friendly management of gene expression data, which are assorted into experimental metadata, experimental design, raw data, normalized details, and analysis results. FFGED functions as a collective and collaborative platform, by connecting each experiment with similar related experiments made public by other users, and correlating diverse gene expression levels under multiple experimental designs within different experiments.12246Thu, 23 May 2013 17:30:34 -0400 http://rfam.sanger.ac.ukThe Rfam database aims to catalogue non-coding RNAs through the use of sequence alignments and statistical profile models known as covariance models.11834Thu, 23 May 2013 08:50:39 -0400 http://www.ebi.ac.uk/gxaThe Gene Expression Atlas is an added-value database providing information about gene expression in different cell types, organism parts, developmental stages, disease states, sample treatments and other biological/experimental conditions. The content of this database derives from curation, re-annotation and statistical analysis of selected data from the ArrayExpress Archive of Functional Genomics Data. A simple interface allows the user to query for differential gene expression either (i) by gene names or attributes such as Gene Ontology terms, or (ii) by biological conditions, e.g. diseases, organism parts or cell types.11726Tue, 21 May 2013 20:00:16 -0400 http://rfam.sanger.ac.uk/Database of structure-annotated multiple sequence alignments, covariance models and family annotation for a number of non-coding RNA families.11385Tue, 14 May 2013 19:00:22 -0400 http://cssb.biology.gatech.edu/skolnick/people/zhou.htmlTools from the Zhou laboratory including predictors of transmembrane topology (THUMBUP, UMDHMM-TMHP, TUPS); prediction/analysis tools for tertiary structure (SPARKS2, SP3); and, prediction/analysis tools for interactions (DMONOMER, DLOOP, DMUTANT, DCOMPLEX, DDNA, TCD, DOGMA).11309Wed, 22 May 2013 15:30:26 -0400 http://lowelab.ucsc.edu/snoscan/Snoscan allows you to search for C/D box methylation guide snoRNA (small nucleolar RNA) genes in a genomic sequence10720Tue, 21 May 2013 11:50:15 -0400 http://prep.unl.edu/The PREP (Predictive RNA Editors for Plants) suite predicts sites of RNA editing based on the principle that editing in plant organelles increases the conservation of proteins across species. Predictors for mitochondrial genes, chloroplast genes, and alignments input by the user are included.10567Mon, 20 May 2013 09:30:12 -0400 http://biowiki.org/XreiProgramxREI is a web interface that allows users to explore a range of predefined phylo-grammars or create their own phylo-grammar. Grammars are visualized via state transition graphs and substitution matrices. xREI is based on xrate, the flexible software tool for modeling structural and phylogenetic variation in multiple sequence alignments.10441Wed, 22 May 2013 19:30:06 -0400 http://probalign.njit.edu/probalign/logineProbalign computes maximal expected accuracy multiple sequence alignments from partition function posterior probabilities. eProbalign also provides a platform to visualize the alignment, generate images, and manipulate the output.10422Thu, 23 May 2013 15:10:43 -0400 http://wishart.biology.ualberta.ca/rci/cgi-bin/rci_cgi_1_d.pyRCI (Random Coil Index) is a method for predicting protein flexibility using secondary chemical shifts.10410Thu, 23 May 2013 08:30:06 -0400 http://knots.mit.edu/KNOTS is a web server that detects knots in protein structures.10408Wed, 22 May 2013 06:10:18 -0400 http://tfam.lcb.uu.se/TFAM is a system to classify the function of tRNAs that is based on tRNA structural alignments.10404Fri, 17 May 2013 02:50:30 -0400 http://ccg.vital-it.ch/madap/MADAP is a clustering tool for the interpretation annotation data mapped onto complete or partial genome sequences. Initially developed for determining transcription start sites (TSS) by defining 5\' and 3\'ends of mRNA, MADAP also has utility in clustering other annotation data types (ChIP-chip data, for example).10394Mon, 20 May 2013 09:00:19 -0400 http://bioportal.weizmann.ac.il/dipol/The Protein Dipole server calculates and displays the net charge, dipole moment and mean radius of any 3-dimensional protein structure.10381Wed, 22 May 2013 02:10:24 -0400 http://compbio.cs.sfu.ca/taverna/taveRNA hosts three RNA web services: alteRNA, inteRNA and pRuNA. alteRNA is an alternative to many RNA folding methods. inteRNA predicts the joint secondary structure of two RNA sequences. pRuNA is an database pruning method which given a query RNA returns only a few ncRNAs as potential regulators.10367Fri, 17 May 2013 17:00:23 -0400 http://www.cs.nuim.ie/distributed/multiphyl.phpMultiPhyl is a high-throughput Maximum Likelihood based phylogeny analysis program that allows researchers to create a virtual phylogenetic supercomputer from a group semi-idle desktop machines.10374Thu, 23 May 2013 03:40:22 -0400 http://wolfpsort.org/WoLF PSORT is an extension of the PSORT II program for protein subcellular location prediction.10353Wed, 22 May 2013 21:00:08 -0400 http://bibiserv.techfak.uni-bielefeld.de/pknotsrg/pknotsRG is a server for single sequence RNA secondary structure prediction including pseudoknots; source code, binary executable, and web service available.10351Sun, 19 May 2013 14:40:28 -0400 http://www.magma-fgcz.unizh.ch/pages/loginuser.jsfMAGMA can be used for the analyses of two-channel microarray experiments and computes genes with significant differential expression using R and Bioconductor. Automatically generated R-scripts are available for download.10350Fri, 17 May 2013 16:30:16 -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.10337Tue, 21 May 2013 17:10:34 -0400 http://pcons.net/Pcons.net is a protein structure prediction meta server that provides automated tools for protein structure prediction and analysis using a consensus approach.10336Thu, 16 May 2013 05:30:43 -0400 http://www.dsimb.inserm.fr/dsimb_tools/peeling3/Protein Peeling is an approach for splitting a protein three dimensional (3D) structure into protein units, an intermediate level of protein structure description between protein domains and secondary structures.10276Tue, 21 May 2013 19:00:17 -0400 http://neuroproteomics.scs.uiuc.edu/neuropred.htmlNeuroPred is a tool designed to predict cleavage sites at basic amino acid locations in neuropeptide precursor sequences. Neuropred also computes the mass of the predicted peptides with or without selected post-translational modifications.10272Tue, 21 May 2013 20:40:23 -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.10241Thu, 23 May 2013 10:00:35 -0400 http://ignm.ccbb.pitt.edu/GNM_Online_Calculation.htmOnline Guassian Network Model (oGNM) calculates the equilibrium dynamics of any structure submitted in PDB format, using the Gaussian Network Model (GNM), a network model for representing biomolecules.10218Thu, 23 May 2013 16:30:33 -0400 http://tubic.tju.edu.cn/GC-Profile/GC-Profile is a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences.10194Sun, 19 May 2013 01:50:36 -0400 http://psfs.cbrc.jp/fold-rate/FOLD-RATE predicts the folding rates of proteins from their amino acid sequences.10192Mon, 20 May 2013 07:20:25 -0400 http://darwin.uvigo.es/software/modeltest_server.htmlModelTest is program for the selection the model of DNA evolution (nucleotide substitution) that best fits your data from phylogenetic analyses.10191Mon, 20 May 2013 03:10:17 -0400 http://www.enzim.hu/index.php?option=com_content&task=blogcategory&id=30&Itemid=92A set of severs developed by the Institute of Enzymology that includes tools for transmembrane protein structure prediction and structural analyses.10187Thu, 23 May 2013 03:30:44 -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.10182Thu, 23 May 2013 08:30:26 -0400 http://stat.genopole.cnrs.fr/spatt/index.htmlStatistics for Patterns (SPatt) can compute the significance of a given DNA pattern in a genome sequence. This tool can be used to find patterns with unusual behaviour in DNA sequences.10126Wed, 22 May 2013 08:30:20 -0400 http://feature.stanford.edu/webfeature/WebFEATURE is a structural analysis tool for identifying 3D physiochemical motifs in molecular structures.10103Thu, 23 May 2013 13:00:42 -0400 http://guinevere.otago.ac.nz/stats.htmlGLUE, PEDEL, and DRIVeR are tools for estimating completeness and diversity in randomized protein-encoding libraries; useful for guiding library design and for analyzing results. GLUE Including Translation (GLUE-IT) finds the expected amino acid completeness of libraries. PEDEL-AA calculates amino acid statistics for libraries generated by epPCR.10083Thu, 23 May 2013 21:30:18 -0400 http://eureka.cbrc.jp/asian/ASIAN (Automatic System for Inferring a Network) is a server for inferring regulatory networks from gene expression profiles that combines cluster analysis, regression analysis, and graphical Gaussian modeling.10000Wed, 22 May 2013 03:10:21 -0400 http://genome.ucsd.edu/microarray/VAMPIRE is a collection of Java tools designed to perform Bayesian statistical analysis of gene expression array data.9985Wed, 22 May 2013 01:20:36 -0400 http://gpcr.biocomp.unibo.it/biodec/TRAMPLE is a tool for the prediction of transmembrane helices, transmembrane strands, secondary structure, and signal peptides.9971Wed, 22 May 2013 15:10:13 -0400 http://bioinformatics.biol.uoa.gr/PRED-TMBB/PRED-TMBB is a tool that takes a Gram-negative bacteria protein sequence as input and predicts the transmembrane strands and the probability of it being an outer membrane beta-barrel protein. The user has a choice of three different decoding methods.9840Sat, 18 May 2013 10:00:33 -0400 http://sfold.wadsworth.orgServer with three tools for the rational design of small interfering RNAs (Sirna), antisense oligonucleotides (Soligo), and trans-cleaving ribozymes (Sribo). A fourth tool, Srna, returns output including general folding features.9820Wed, 22 May 2013 12:10:43 -0400 http://genes.mit.edu/McPromoter.htmlThe Markov Chain Promoter Prediction Server (McPromoter) uses statistics to predict eukaryotic DNA transcription start sites.9776Fri, 17 May 2013 14:30:06 -0400 http://genes.cs.wustl.edu/Twinscan is a system for predicting gene-structure in eukaryotic genomic sequences. In order to make its predictions, Twinscan combines the information from predicted coding regions and splice sites with conserservation measurements between the target sequence and sequences from a closely related genome. Currently sequences from mammalian genomes, and those of Arabidopsis thaliana, C. elegans, C. briggsae and strains JEC21 and H99 of Cryptococcus neoformans can be processed using Twinscan.9766Wed, 22 May 2013 10:10:20 -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.9425Mon, 20 May 2013 22:20:11 -0400 http://biwww3.informatik.uni-freiburg.de:8080/BioBayesNet/BioBayesNet is a server for feature extraction and Bayesian network modeling of biological sequence data.9270Wed, 22 May 2013 10:30:17 -0400 http://bond.unleashedinformatics.com/Action?Stores full descriptions of interactions, molecular complexes and pathways; researchers are able to submit new records.9267Mon, 20 May 2013 03:30:22 -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.9265Wed, 22 May 2013 19:00:10 -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.9254Wed, 22 May 2013 19:40:13 -0400 http://asterias.bioinfo.cnio.es/Asterias is a set of tools for the analyses of high throughput genomic data that includes applications for microarray data normalization, filtering, detection of differential gene expression, class and survival prediction model building, and analysis of array CGH data. Most applications use parallel computing resulting in significant increases in speed.9251Mon, 20 May 2013 08:10:07 -0400 http://enm.lobos.nih.govAnalysis of Dynamics of Elastic Network Model (AD-ENM) predicts the conformational changes a given protein structure can undergo.9217Tue, 21 May 2013 16:40:08 -0400 http://3dlogo.uniroma2.it/3dLOGO/home.html3dLOGO is a server for the identification and analysis of conserved protein three-dimensional (3D) substructures.9209Tue, 21 May 2013 05:50:23 -0400