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Links tagged with 'markov chains'

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Found 40 links

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Affymetrix NetAffx Analysis CenterDatabase Content

http://www.affymetrix.com/analysis/index.affx

Expression > Transcript Expression Analysis

Allows correlation of GeneChip array results with array design and annotation information; provides access to array content information, including probe sequences and gene annotations; free registration is required.

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tagsanimals consensus sequence gene expression profiling genetic databases markov chains oligonucleotide array sequence analysis protein sequence analysis proteins

AMIGeneTool Content

http://www.genoscope.cns.fr/agc/tools/amigene/Form/form.php

DNA > Gene Prediction
Model Organisms > Microbes

Annotation of MIcrobial Genes (AMIGene) is gene prediction server that can identify coding sequences in microbes.

NAR Web Server Issue 2003
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tagsbacterial dna bacterial genes dna sequence analysis markov chains open reading frames

AUGUSTUSTool Content

http://bioinf.uni-greifswald.de/augustus

DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Expression > Splicing
Protein > Domains and Motifs

AUGUSTUS 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.

This content is being maintained by Mario Stanke.

NAR Web Server Issue 2004NAR Web Server Issue 2005NAR Web Server Issue 2006
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tagsadult algorithms alternative splicing animals artificial intelligence automated pattern recognition base sequence bile acids and salts cholic acids chromosome mapping computer simulation deoxycholic acid dna sequence analysis drosophila melanogaster exons female gene components gene expression genes genetic databases genetic models genetic variation genomics human genome humans hypercholesterolemia hyperlipidemias introns ldl lipoproteins male markov chains middle aged molecular sequence data proteins sequence alignment statistical models stochastic processes triglycerides vldl lipoproteins

Berkeley Phylogenomics GroupTool Content

http://phylogenomics.berkeley.edu/

DNA > Phylogeny Reconstruction
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments

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.

NAR Web Server Issue 2007
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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals artificial intelligence bayes theorem binding sites computational biology gene expression profiling genetic databases genetic models humans likelihood functions markov chains molecular evolution molecular sequence data phylogeny protein conformation protein databases protein sequence analysis proteins reproducibility of results sensitivity and specificity sequence alignment src homology domains statistical models tertiary protein structure time factors

BioProspectorTool Content

http://robotics.stanford.edu/~xsliu/BioProspector/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis

Server which scans upstream of genes in the same gene expression cluster for regulatory sequence motifs using a Gibbs sampling strategy. The Markov background model is used for non-motif bases, improving specificity of predicted motif locations.

NAR Web Server Issue 2004
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tagsalgorithms bacillus subtilis base sequence binding sites carrier proteins conserved sequence cyclic amp receptor protein dna escherichia coli gene expression profiling gene expression regulation genetic models genetic transcription markov chains nucleic acid regulatory sequences oligonucleotide array sequence analysis rap1 gtp-binding proteins regulator genes saccharomyces cerevisiae sequence alignment tata box transcription factors

FISHTool Content

http://max.ucmp.umu.se/sahmm/

Protein > 3-D Structure Retrieval/Viewing
Protein > Domains and Motifs
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Family Identification with Structure Anchored HMMs (FISH) is a server for the identification of remote sequence homologues on the basis of protein domains.

NAR Web Server Issue 2006
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tagsamino acid sequence homology markov chains protein databases tertiary protein structure

Gene3DDatabase Content

http://gene3d.biochem.ucl.ac.uk/

Protein > Databases

Gene3D provides accurate structural domain family assignments for over 1100 genomes and nearly 10,000,000 proteins. A hidden Markov model library, constructed from the manually curated CATH structural domain hierarchy, is used to search UniProt, RefSeq and Ensembl protein sequences. The resulting matches are refined into simple multi-domain architectures. The domain assignments are integrated with multiple external protein function descriptions (e.g. Gene Ontology and KEGG), structural annotations (e.g. coiled coils, disordered regions and sequence polymorphisms) and family resources (e.g. Pfam and eggNog). Gene3D also provides a set of services, including an interactive genome coverage graph visualizer, DAS annotation resources, sequence search facilities and SOAP services.

NAR Database Issue 2010
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tagsalgorithms animals archaeal genome bacterial genome computational biology dna sequence analysis genetic databases humans markov chains nucleic acid databases protein databases tertiary protein structure viral genome

GeneMarkTool Content

http://opal.biology.gatech.edu/GeneMark/

DNA > Gene Prediction

The GeneMark family of programs employ Markov models and are specifically tuned for gene prediction for sequences from prokaryotes, viral genomes and eukaryotes.

NAR Web Server Issue 2005
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tagsalgorithms animals bacterial genes computational biology genes genomics humans markov chains viral genes

GENSCANTool Content

http://genes.mit.edu/GENSCAN.html

DNA > Gene Prediction

Identification of complete gene structures in genomic DNA.

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tagsanimals dna dna sequence analysis exons genes genetic models genetic promoter regions genetic techniques genetic transcription human genome humans introns markov chains molecular sequence data nucleic acid repetitive sequences probability protein biosynthesis proteins rna splicing vertebrates

Gibbs Motif SamplerTool Content

http://ccmbweb.ccv.brown.edu/gibbs/gibbs.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > Domains and Motifs

Gibbs Motif Sampler allows you to identify motifs, conserved regions, in DNA or protein sequences. This tool can be applied for the detection of transcription factor binding sites (TFBS).

This content is being maintained by bbth.

NAR Web Server Issue 2003NAR Web Server Issue 2007
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tagsalgorithms amino acid sequence animals bacterial dna bacterial genes bacterial genome bacterial outer membrane proteins base sequence binding sites biological evolution carrier proteins chemical models computational biology consensus sequence dna sequence analysis escherichia coli factual databases gammaproteobacteria gene expression regulation genetic models genetic transcription genetic variation helix-loop-helix motifs homology human genome humans markov chains mice molecular sequence data monte carlo method nonparametric statistics nucleic acid regulatory sequences nucleic acid repetitive sequences nucleic acid sequence homology phylogeny protein binding protein prenylation secondary protein structure sequence alignment skeletal muscle statistical models transcription factors transcription initiation site transferases

GlimmerTool Content

http://cbcb.umd.edu/software/glimmer/

DNA > Gene Prediction

Gene Locator and Interpolated Markov Modeler; this prokaryote-gene finding tool is the primary microbial gene finder used at TIGR; free (including source code) with registration for non-commercial use.

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tagsalgorithms animals artifacts bacterial dna bacterial genes bacterial genome base sequence chromosome mapping decapodiformes dna sequence analysis genetic models genetic techniques haemophilus influenzae helicobacter pylori markov chains open reading frames prochloron reproducibility of results sensitivity and specificity sequence alignment symbiosis

GRIFFINTool Content

http://griffin.cbrc.jp/

Protein > Annotation and Function

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.

NAR Web Server Issue 2005
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tagsartificial intelligence g-protein-coupled receptors heterotrimeric gtp-binding proteins ligands markov chains protein sequence analysis

HHpredTool Content

http://protevo.eb.tuebingen.mpg.de/hhpred

Protein > 3-D Structure Comparison
Protein > 3-D Structure Prediction
Sequence Comparison > Similarity Searching

Based on the comparison of profile HMMs, HHpred takes a protein sequence or multiple sequence alignment as input and searches for remote homologues in an assortment of databases such as PDB, SMART and Pfam. The user can select either a local or global alignment method, and the search results can be used to generate 3D structural models.

NAR Web Server Issue 2005
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tagsamino acid sequence homology bacterial proteins markov chains protein conformation protein databases protein sequence analysis sequence alignment transcription factors

HHrepTool Content

http://toolkit.tuebingen.mpg.de/hhrep

Protein > 2-D Structure Prediction
Protein > Sequence Features
Sequence Comparison > Other Alignment Tools
Sequence Comparison > Similarity Searching

HHrep is a tool for the de novo identification of repeats in protein sequences based on the pairwise comparison of profile hidden Markov models (HMMs).

NAR Web Server Issue 2006
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tagsamino acid repetitive sequences markov chains protein folding protein sequence analysis sequence alignment

HHsenserTool Content

http://toolkit.tuebingen.mpg.de/hhsenser

Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

HHsenser is a tool for sensitive iterative sequence searching based on HMM-HMM comparison. Starting from a single sequence or an alignment, HHSenser is able to build alignments with as many near or remote homologs as possible allowing users to explore protein superfamilies.

NAR Web Server Issue 2006
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tagsamino acid sequence homology markov chains protein sequence analysis sequence alignment sequence analysis