> Tag > Links tagged with 'dna methylation'

Links tagged with 'dna methylation'

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BiQ Analyzer HTTool Content

http://biq-analyzer-ht.bioinf.mpi-inf.mpg.de/ [open in a new window]

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DNA > DNA and Genomic Analysis

BiQ Analyzer HT Is a tool that supports locus specific analysis and visualization of high-throughput bisulfite sequencing data. It facilitates analysis of locus specific DNA methylation patterns.

links directory index: 225
TitlePublication YearGoogle Scholar Citation Count
BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing20114
BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing2005221
NAR Web Server Issue 2011
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tagsdna dna methylation dna sequence analysis genetic loci high-throughput nucleotide sequencing polymerase chain reaction sequence alignment sulfites

HHMDDatabase Content

http://bioinfo.hrbmu.edu.cn/hhmd [open in a new window]

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Protein > Databases

Human Histone Modification Database (HHMD) focuses on the storage and integration of histone modification datasets that were obtained from laboratory experiments. HHMD incorporates 43 location-specific histone modifications in human. HHMD can be searched by histone modification, gene ID, functional categories, chromosome location and cancer name. HHMD also includes a user-friendly visualization tool named HisModView, by which genome-wide histone modification map can be shown.

links directory index: 16
TitlePublication YearGoogle Scholar Citation Count
HHMD: the human histone modification database201016
NAR Database Issue 2010
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tagsalgorithms chromatin chromatin immunoprecipitation computational biology dna methylation gene expression profiling genetic databases histones humans protein databases

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

NGSmethDBDatabase Content

http://bioinfo2.ugr.es/NGSmethDB/gbrowse/ [open in a new window]

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DNA > Databases

NGSmethDB contains methylation data derived from next-generation sequencing (NGS). Two cytosine methylation contexts (CpG and CAG/CTG) are considered. Through a browser interface, the user can search for methylation states in a set of tissues, retrieve methylation values for a set of tissues in a given chromosomal region, or display the methylation of promoters among different tissues. NGSmethDB is currently populated with human, mouse and Arabidopsis data.

links directory index: 8
TitlePublication YearGoogle Scholar Citation Count
NGSmethDB: a database for next-generation sequencing single-cytosine-resolution DNA methylation data20118
NAR Database Issue 2011
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external linksLink on Wikipedia
tagsanimals chromosomes cpg islands cytosine data mining dna methylation dna sequence analysis genetic promoter regions genomics humans mice nucleic acid databases

QUMATool Content

http://quma.cdb.riken.jp/ [open in a new window]

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DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms

Quantification tool for Methylation Analysis (QUMA) is a web-based bisulfite sequencing analysis tool for CpG methylation analysis. Following user input of PCR target genomic sequence and raw bisulfite sequences, alignment, visualization and quantification of the bisulfite sequence data is rapid. Users can also control the quality of aligned sequences by changing cutoff paramteres.

links directory index: 61
TitlePublication YearGoogle Scholar Citation Count
QUMA: quantification tool for methylation analysis200861
NAR Web Server Issue 2008
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tagscpg islands dna methylation dna sequence analysis statistical data interpretation sulfites

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