> Tag > Links tagged with 'high-throughput nucleotide sequencing'

Links tagged with 'high-throughput nucleotide sequencing'

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ArrayExpress updateDatabase Content

http://www.ebi.ac.uk/arrayexpress [open in a new window]

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Expression > Databases

The ArrayExpress Archive is a public repository of functional genomics data supporting publications. It includes data generated by sequencing or array-based technologies. Data are submitted by users and imported directly from the NCBI Gene Expression Omnibus. The ArrayExpress Archive is closely integrated with the Gene Expression Atlas and the sequence databases at the European Bioinformatics Institute. Advanced queries provided via ontology enabled interfaces include queries based on technology and sample attributes such as disease, cell types and anatomy.

links directory index: 60
TitlePublication YearGoogle Scholar Citation Count
ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments201160
NAR Database Issue 2011
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tagsgene expression gene expression profiling genetic databases genomics high-throughput nucleotide sequencing oligonucleotide array sequence analysis

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

ChIP-ArrayTool Content

http://wanglab.hku.hk/ChIP-Array [open in a new window]

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Expression > Gene Regulation

ChIP-Array is a web server that integrates ChIP-seq and microarray gene expression data to discover direct and indirect target genes regulated by a transcription factor of interest.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor20113
NAR Web Server Issue 2011
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tagsanimals binding sites chromatin immunoprecipitation gene expression profiling high-throughput nucleotide sequencing humans mice oligonucleotide array sequence analysis transcription factors transcriptional regulatory elements

CNVerTool Content

http://compbio.cs.toronto.edu/cnver/ [open in a new window]

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Human Genome > Sequence Polymorphisms
Sequence Comparison > Pairwise Sequence Alignments

CNVer is a method for CNV detection that supplements the depth-of-coverage with paired-end mapping information, where matepairs mapping discordantly to the reference serve to indicate the presence of variation. CNVer combines this information within a unified computational framework called the donor graph, allowing it to better mitigate the sequencing biases that cause uneven local coverage.

links directory index: 23
TitlePublication YearGoogle Scholar Citation Count
Detecting copy number variation with mated short reads201023
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tagsalgorithms base pairing base sequence chromosome breakage chromosome mapping dna copy number variations dna mutational analysis dna shuffling high-throughput nucleotide sequencing humans reproducibility of results
setsUniversity of Toronto

inGAP-svTool Content

http://ingap.sourceforge.net [open in a new window]

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DNA > Sequence Polymorphisms

inGAP-sv is a web server to identify and visualize structural variation from paired end mapping data. Several important features including local depth of coverage, mapping quality and associated tandem repeats are used to evaluate the quality of the predicted structural variation.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
inGAP-sv: a novel scheme to identify and visualize structural variation from paired end mapping data20111
NAR Web Server Issue 2011
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tagschromosome aberrations chromosome mapping computer simulation dna sequence analysis genetic variation high-throughput nucleotide sequencing indel mutation

PRI-CATTool Content

http://www.ab.wur.nl/pricat [open in a new window]

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Computer Related > Workflows
Expression > Gene Regulation
Model Organisms > Plants

PRI-CAT is a web-based workflow tool for the management and analysis of plant ChIP-seq experiments, with focus on Arabidopsis. Secondary analysis can be performed with the aid of GALAXY.

This content is being maintained by jose.muino@wur.nl.

links directory index: 5
TitlePublication YearGoogle Scholar Citation Count
PRI-CAT: a web-tool for the analysis, storage and visualization of plant ChIP-seq experiments20115
NAR Web Server Issue 2011
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tagsarabidopsis binding sites ChIP-seq chromatin immunoprecipitation dna-binding proteins genetic promoter regions high-throughput nucleotide sequencing plant proteins plants transcription factors

SRADatabase Content

http://www.ncbi.nlm.nih.gov/Traces/sra [open in a new window]

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DNA > Databases

The Sequence Read Archive (SRA) was established as a public repository for the next-generation sequence data and is operated by the International Nucleotide Sequence Database Collaboration (INSDC). INSDC partners include the National Center for Biotechnology Information (NCBI), the European Bioinformatics Institute (EBI) and the DNA Data Bank of Japan (DDBJ).

This content is being maintained by rasko.

links directory index: 39
TitlePublication YearGoogle Scholar Citation Count
The Sequence Read Archive: explosive growth of sequencing data20126
The sequence read archive201133
NAR Database Issue 2011
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tagshigh-throughput nucleotide sequencing nucleic acid databases

TIARADatabase Content

http://tiara.gmi.ac.kr [open in a new window]

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DNA > Databases
Human Genome > Databases

Total Integrated Archive of Short-Read and Array (TIARA) database, contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs).

links directory index: 4
TitlePublication YearGoogle Scholar Citation Count
TIARA: a database for accurate analysis of multiple personal genomes based on cross-technology20114
NAR Database Issue 2011
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tagsdna sequence analysis genetic variation genomics high-throughput nucleotide sequencing human genome humans nucleic acid databases nucleic acid hybridization

WormBaseDatabase Content

http://www.wormbase.org/ [open in a new window]

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Model Organisms > Worm

Repository of mapping, sequencing and phenotypic information about C. elegans and C. briggsae.

links directory index: 206
TitlePublication YearGoogle Scholar Citation Count
WormBase: a comprehensive resource for nematode research201099
WormBase: a cross-species database for comparative genomics2003107
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external linksLink on Twitter Link on Wikipedia
tagsalleles animals base sequence caenorhabditis caenorhabditis elegans computational biology data collection expressed sequence tags gene expression genetic databases genomics helminth dna helminth genes helminth rna high-throughput nucleotide sequencing information storage and retrieval intergenic dna internet molecular sequence annotation neurons nucleic acid databases nucleic acid sequence homology open reading frames phenotype protein databases quality control rna interference single nucleotide polymorphism software tertiary protein structure transcription factors

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