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Links tagged with 'genomics'

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UCSC Cancer Genomics BrowserDatabase Content

https://genome-cancer.ucsc.edu [open in a new window]

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Human Genome > Genomics
Human Genome > Health and Disease

The UCSC Cancer Genomics Browser comprises a suite of web-based tools to integrate, visualize and analyze cancer genomics and clinical data. The browser displays whole-genome views of genome-wide experimental measurements for multiple samples alongside their associated clinical information. Multiple data sets can be viewed simultaneously as coordinated 'heatmap tracks' to compare across studies or different data modalities. Users can order, filter, aggregate, classify and display data interactively based on any given feature set including clinical features, annotated biological pathways and user-contributed collections of genes. Integrated standard statistical tools provide dynamic quantitative analysis within all available data sets. Many new features have been added, including the hgMicroscope tumor image viewer, hgSignature for real-time genomic signature evaluation on any browser track, and 'PARADIGM' pathway tracks to display integrative pathway activities.

This content is being maintained by jzhu.

links directory index: 12
TitlePublication YearGoogle Scholar Citation Count
The UCSC Cancer Genomics Browser: update 2011201112
NAR Database Issue 2011
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tagsdna copy number variations gene expression genetic databases genomics human genome humans neoplasms

UCSC Genome BrowserDatabase Content

http://genome.ucsc.edu/ [open in a new window]

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DNA > Databases
Human Genome > Databases
Model Organisms > Databases

The University of California, Santa Cruz (UCSC) Genome Browser website provides a large database of publicly available sequence and annotation data along with an integrated tool set for examining and comparing the genomes of organisms, aligning sequence to genomes, and displaying and sharing users' own annotation data. Genomic sequence and a basic set of annotation 'tracks' are provided for organisms, including mammals, non-mammal vertebrates, invertebrate deuterostomes, insects, worms and yeast. New features include drag-and-zoom navigation, a Wiki track for user-added annotations, new custom track formats for large datasets (bigBed and bigWig), a new multiple alignment output tool, links to variation and protein structure tools, in silico PCR utility enhancements, and improved track configuration tools.

links directory index: 424
TitlePublication YearGoogle Scholar Citation Count
The UCSC Genome Browser database: extensions and updates 2011201211
ENCODE whole-genome data in the UCSC Genome Browser: update 2012201286
The UCSC Genome Browser database: update 20102010327
NAR Database Issue 2010
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tagsanimals computational biology fungal genome genetic databases genetic variation genome genomics humans invertebrates molecular models nucleic acid databases phenotype

UCSC SARS Genome Browser GatewayTool Content

http://genome.ucsc.edu/cgi-bin/hgGateway?org=SARS&db=0&hgsid=27736277 [open in a new window]

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Model Organisms > Other Organisms

Provides a rapid and reliable display of any requested portion of the SARS genome at any scale, together with dozens of aligned annotation tracks.

links directory index: 1185
TitlePublication YearGoogle Scholar Citation Count
The UCSC Genome Browser Database20031185
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tagsanimals california database management systems genetic databases genomics human genome humans mice

VelvetTool Content

http://www.ebi.ac.uk/~zerbino/velvet/ [open in a new window]

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DNA > Mapping and Assembly

Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454. Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs.

links directory index: 924
TitlePublication YearGoogle Scholar Citation Count
Velvet: algorithms for de novo short read assembly using de Bruijn graphs2008924
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tagsalgorithms animals artificial chromosomes bacterial genome computational biology computer simulation dna sequence analysis genomics human genome humans mammals streptococcus

ViralZoneDatabase Content

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

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Model Organisms > Databases

ViralZone web resource provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increase of virus sequences. ViralZone offers a complete set of detailed and accurate virion pictures.

links directory index: 2
TitlePublication YearGoogle Scholar Citation Count
ViralZone: a knowledge resource to understand virus diversity20112
NAR Database Issue 2011
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tagsgenetic databases genomics proteomics viral genome viral proteins virion virus physiological phenomena virus replication viruses

VIRGOTool Content

http://whipple.cs.vt.edu/virgoperl/welcome.cgi [open in a new window]

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DNA > Annotations
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Human Genome > Annotations
Model Organisms > Yeast
Protein > Annotation and Function
Protein > Networks & Interactions, Pathways and Enzymes

Virtual Gene Ontology (VIRGO) provides gene function predictions for yeast and human by constructing a functional linkage network (FLN) from gene expression and molecular interaction data. VIRGO then labels genes in the FLN with their annotations from Gene Ontology, and systematically propagates these labels across the FLN in order to predict the functions of unlabelled genes.

links directory index: 237
TitlePublication YearGoogle Scholar Citation Count
VIRGO: computational prediction of gene functions200620
Whole-genome annotation by using evidence integration in functional-linkage networks2004217
NAR Web Server Issue 2006
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tagsalgorithms biological models chromosome mapping computational biology controlled vocabulary gene expression genes genomics humans neural networks (computer) oligonucleotide array sequence analysis reproducibility of results saccharomyces cerevisiae

VOMBATTool Content

https://www2.informatik.uni-halle.de:8443/VOMBAT/faces/pages/choose.jsp [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

VOMBAT predicts transcription factor binding sites (TFBS) and other motifs in sequence data based on Variable Order Markov models and variable order BAyesian Trees.

links directory index: 99
TitlePublication YearGoogle Scholar Citation Count
VOMBAT: prediction of transcription factor binding sites using variable order Bayesian trees20069
Identification of transcription factor binding sites with variable-order Bayesian networks200590
NAR Web Server Issue 2006
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tagsalgorithms artificial intelligence bayes theorem binding sites chemical models computer simulation genomics markov chains molecular models protein binding protein databases protein sequence analysis sequence alignment statistical models structure-activity relationship transcription factors transcriptional regulatory elements

waviCGHTool Content

http://wavi.bioinfo.cnio.es [open in a new window]

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DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms
Model Organisms > Mouse and Rat

waviCGH is a web server for the analysis and comparison of genomic copy number alterations in multiple same species samples. For human, mouse and rat genomes, results are mapped back onto the genome.

links directory index: 7
TitlePublication YearGoogle Scholar Citation Count
waviCGH: a web application for the analysis and visualization of genomic copy number alterations20107
NAR Web Server Issue 2010
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tagsanimals comparative genomic hybridization dna copy number variations genomics humans mice oligonucleotide array sequence analysis rats

WebFEATURETool Content

http://feature.stanford.edu/webfeature/ [open in a new window]

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Protein > 3-D Structural Features
Protein > Domains and Motifs
RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

WebFEATURE is a structural analysis tool for identifying 3D physiochemical motifs in molecular structures.

links directory index: 121
TitlePublication YearGoogle Scholar Citation Count
WebFEATURE: An interactive web tool for identifying and visualizing functional sites on macromolecular structures200364
Recognizing protein binding sites using statistical descriptions of their 3D environments199857
NAR Web Server Issue 2003
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tagsalgorithms bayes theorem binding sites calcium calcium-binding proteins computational biology factual databases genomics likelihood functions macromolecular substances molecular models molecular structure nucleic acid conformation nucleic acids protein conformation proteins reproducibility of results sensitivity and specificity statistical models

WebGMAPTool Content

http://www.bioinfolab.org/software/webgmap [open in a new window]

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Expression > cDNA, EST, SAGE
Human Genome > Genomics
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Pairwise Sequence Alignments

A web server with a suite of tools for cDNA-genome alignment, visualization and mining. The sequence viewer allows for nucleotide positioning, 6-frame translations, sequence reverse complementation and imperfect motif detection and alignment. Users can also sort, filter and search for individual cDNA sequences or alignments.

links directory index: 2
TitlePublication YearGoogle Scholar Citation Count
WebGMAP: a web service for mapping and aligning cDNA sequences to genomes20092
NAR Web Server Issue 2009
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tagschromosome mapping complementary dna dna sequence analysis genomics sequence alignment

WebMAMTool Content

http://compbio.cs.sfu.ca/MAM.htm [open in a new window]

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Sequence Comparison > Analysis of Aligned Sequences

This is the web version of the Multiple alignment Manipulator (MaM), which takes a multiple alignment of genomic sequences as input and calculates the locations of exons, common repeat elements and unique regions based on user-selected programs/information. The graphical display also allows users to focus an assessment of sequence variation on the identified regions.

links directory index: 7
TitlePublication YearGoogle Scholar Citation Count
Manipulating multiple sequence alignments via MaM and WebMaM20057
NAR Web Server Issue 2005
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tagsexons genomics nucleic acid repetitive sequences phylogeny sequence alignment

WebScipio - eukaryotic gene identificationTool Content

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

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DNA > Gene Prediction
Expression > Splicing
RNA > General Resources
Sequence Comparison > Analysis of Aligned Sequences

Scipio is a tool to determine the precise exon-intron gene structure given a protein sequence and a genome. It identifies splice sites and is able to cope with sequencing errors and genes spanning several contigs. The output contains information about discrepancies that may result from sequencing errors. Scipio has also successfully been used to find homologous genes in related species. WebScipio, allows to search for mutually exclusive spliced exons and tandemly arrayed gene duplicates.

links directory index: 24
TitlePublication YearGoogle Scholar Citation Count
WebScipio: an online tool for the determination of gene structures using protein sequences20089
Scipio: using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species200815
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tagsacetylcholine action potentials algorithms alternative splicing amino acid sequence animals apomorphine atropine base sequence benserazide bromocriptine central nervous system dextroamphetamine diaphragm dna sequence analysis dopamine drosophila melanogaster drosophila proteins epinephrine exon-intron structure exons extrapyramidal tracts female gene duplicates gene prediction gene structure genetic databases genomics haloperidol human parainfluenza virus 3 humans hydroxylamines immunologic deficiency syndromes infant introns kinetics levodopa mathematics molecular sequence data motor activity muscle contraction muscle denervation mutually exclusive splicing nerve degeneration neurological models neuromuscular junction nucleic acid sequence homology oxidation-reduction paramyxoviridae infections physostigmine piribedil planarians protein sequence analysis proteins rats reading frames reserpine rna splice sites sequence alignment software species specificity superoxide dismutase superoxides synaptic transmission tandem gene duplication tetrodotoxin turbellaria user-computer interface viral pneumonia x chromosome

WEGOTool Content

http://wego.genomics.org.cn/cgi-bin/wego/index.pl [open in a new window]

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DNA > Annotations
Human Genome > Annotations
Model Organisms > General Resources
Protein > Annotation and Function

Web Gene Ontology Annotation Plot (WEGO) helps visualize the annotation of sets of genes. WEGO can compare gene annotation datasets by plotting the distribution of gene ontology (GO) annotation results into a histogram.

links directory index: 116
TitlePublication YearGoogle Scholar Citation Count
WEGO: a web tool for plotting GO annotations2006116
NAR Web Server Issue 2006
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tagscontrolled vocabulary genes genomics

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

ZFINDatabase Content

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

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Model Organisms > Databases
Model Organisms > Fish

ZFIN, the Zebrafish Model Organism Database serves as the central repository and web-based resource for zebrafish genetic, genomic, phenotypic and developmental data. ZFIN manually curates comprehensive data for zebrafish genes, phenotypes, genotypes, gene expression, antibodies, anatomical structures and publications. A wide-ranging collection of web-based search forms and tools facilitates access to integrated views of these data promoting analysis and scientific discovery. Data formats include text, images and graphical representations.

links directory index: 17
TitlePublication YearGoogle Scholar Citation Count
ZFIN: enhancements and updates to the Zebrafish Model Organism Database201117
NAR Database Issue 2011
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tagsanimal models animals antibodies gene expression genetic databases genomics messenger rna phenotype zebrafish

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