> Tag > Links tagged with 'markov chains'

Links tagged with 'markov chains'

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Found 33 links

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Affymetrix NetAffx Analysis CenterDatabase Content

http://www.affymetrix.com/analysis/index.affx [open in a new window]

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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.

links directory index: 448
TitlePublication YearGoogle Scholar Citation Count
NetAffx: Affymetrix probesets and annotations2003448
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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 [open in a new window]

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DNA > Gene Prediction
Model Organisms > Microbes

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

links directory index: 70
TitlePublication YearGoogle Scholar Citation Count
AMIGene: Annotation of MIcrobial Genes200370
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 [open in a new window]

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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.

links directory index: 233
TitlePublication YearGoogle Scholar Citation Count
Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources200687
AUGUSTUS: ab initio prediction of alternative transcripts200650
AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints200534
AUGUSTUS: a web server for gene finding in eukaryotes200461
The formation of deoxycholic acid in patients with type II and IV hyperlipoproteinaemia19761
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/ [open in a new window]

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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.

This content is being maintained by kimmen.

links directory index: 4963
TitlePublication YearGoogle Scholar Citation Count
Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis200720
MUSCLE: multiple sequence alignment with high accuracy and high throughput20044855
SATCHMO: sequence alignment and tree construction using hidden Markov models200388
Phylogenetic inference in protein superfamilies: analysis of SH2 domains.19980
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/ [open in a new window]

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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.

links directory index: 702
TitlePublication YearGoogle Scholar Citation Count
A suite of web-based programs to search for transcriptional regulatory motifs200432
BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes2001670
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

Gene3DDatabase Content

http://gene3d.biochem.ucl.ac.uk/ [open in a new window]

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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.

links directory index: 22
TitlePublication YearGoogle Scholar Citation Count
Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis.20122
Gene3D: merging structure and function for a Thousand genomes201020
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

GENSCANTool Content

http://genes.mit.edu/GENSCAN.html [open in a new window]

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DNA > Gene Prediction

Identification of complete gene structures in genomic DNA.

links directory index: 3198
TitlePublication YearGoogle Scholar Citation Count
Finding the genes in genomic DNA1998404
Prediction of complete gene structures in human genomic DNA19972794
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external linksLink on Wikipedia
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

GlimmerTool Content

http://cbcb.umd.edu/software/glimmer/ [open in a new window]

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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.

links directory index: 2291
TitlePublication YearGoogle Scholar Citation Count
Identifying bacterial genes and endosymbiont DNA with Glimmer2007403
Improved microbial gene identification with GLIMMER19991199
Microbial gene identification using interpolated Markov models1998689
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external linksLink on Wikipedia
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/ [open in a new window]

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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.

links directory index: 41
TitlePublication YearGoogle Scholar Citation Count
GRIFFIN: a system for predicting GPCR-G-protein coupling selectivity using a support vector machine and a hidden Markov model200541
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 [open in a new window]

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

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.

links directory index: 539
TitlePublication YearGoogle Scholar Citation Count
The HHpred interactive server for protein homology detection and structure prediction2005539
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

HMMERTool Content

http://bioweb.pasteur.fr/seqanal/motif/hmmer-uk.html [open in a new window]

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Sequence Comparison > Similarity Searching and Classification

HMMER is an implementation of profile HMM methods for sensitive database searches using multiple sequence alignments as queries.

links directory index: 2798
TitlePublication YearGoogle Scholar Citation Count
Profile hidden Markov models19982798
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external linksLink on Wikipedia
tagshumans markov chains peptide library sequence alignment

HMMER Web ServerTool Content

http://hmmer.janelia.org [open in a new window]

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Protein > Sequence Comparison
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Other Alignment Tools
Sequence Comparison > Similarity Searching and Classification

HMMER Web Server is a tool for interactive sequence similarity searching. Methods are available for single protein sequence, multiple protein sequence alignment or profile HMM against a target sequence databases, and for searching a protein sequence against Pfam.

links directory index: 24
TitlePublication YearGoogle Scholar Citation Count
HMMER web server: interactive sequence similarity searching201124
NAR Web Server Issue 2011
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external linksLink on Twitter Link on Wikipedia
tagsalgorithms computational biology information storage and retrieval internet markov chains protein databases protein sequence analysis sequence alignment software

HMMgeneTool Content

http://genome.cbs.dtu.dk/services/HMMgene/ [open in a new window]

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DNA > Gene Prediction

Prediction of vertebrate and C. elegans genes.

links directory index: 96
TitlePublication YearGoogle Scholar Citation Count
Using database matches with for HMMGene for automated gene detection in Drosophila200096
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tagsalcohol dehydrogenase animals computational biology computer-assisted numerical analysis drosophila melanogaster factual databases insect genes markov chains nucleic acid sequence homology sensitivity and specificity

Institute of Enzymology ServersTool Content

http://www.enzim.hu/index.php?option=com_content&task=blogcategory&id=30&Itemid=... [open in a new window]

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Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Localization and Targeting

A set of severs developed by the Institute of Enzymology that includes tools for transmembrane protein structure prediction and structural analyses.

links directory index: 2004
TitlePublication YearGoogle Scholar Citation Count
TMDET: web server for detecting transmembrane regions of proteins by using their 3D coordinates200546
IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content2005392
The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins2005235
BiSearch: primer-design and search tool for PCR on bisulfite-treated genomes200552
PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank2005138
Transmembrane proteins in the Protein Data Bank: identification and classification2004138
Locating the stabilizing residues in (alpha/beta)8 barrel proteins based on hydrophobicity, long-range interactions, and sequence conservation200443
SCide: identification of stabilization centers in proteins.20030
Servers for sequence-structure relationship analysis and prediction20035
On filtering false positive transmembrane protein predictions200257
The HMMTOP transmembrane topology prediction server.20010
Principles governing amino acid composition of integral membrane proteins: application to topology prediction1998795
Stabilization centers in proteins: identification, characterization and predictions1997103
NAR Web Server Issue 2003
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tagsalgorithms amino acid sequence amino acids binding sites capsid proteins cell line chemical models computational biology computer simulation conserved sequence cysteine database management systems dna methylation dna primers drug stability energy transfer genome genomics humans hydrophobic and hydrophilic interactions kringles lipid bilayers markov chains membrane proteins molecular models molecular sequence data neural networks (computer) oxidation-reduction pliability polymerase chain reaction protein binding protein conformation protein databases protein engineering protein folding protein sequence analysis proteins reproducibility of results secondary protein structure sequence alignment statistical models structure-activity relationship sulfites temperature tertiary protein structure thermodynamics tissue plasminogen activator

KinasePhos 2.0Tool Content

http://kinasephos2.mbc.nctu.edu.tw/ [open in a new window]

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Protein > Domains and Motifs

KinasePhos 2.0 is a new version of a kinase-specific phosphorylation site prediction tool.

links directory index: 66
TitlePublication YearGoogle Scholar Citation Count
KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns200766
NAR Web Server Issue 2007
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tagscatalytic domain computational biology computer simulation markov chains neural networks (computer) phosphoproteins phosphorylation probability protein kinases protein sequence analysis sensitivity and specificity

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