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Links tagged with 'genetic variation'

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Found 38 links

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ASPicDBDatabase Content

http://www.caspur.it/ASPicDB/

Human Genome > Databases
Protein > Databases

ASPicDB provides a unique annotation resource of human protein variants generated by alternative splicing. A total of 256,939 protein variants from 17,191 multi-exon genes have been extensively annotated through machine learning tools providing information of the protein type (globular and transmembrane), localization, presence of PFAM domains, signal peptides, GPI-anchor propeptides, transmembrane and coiled-coil segments. Furthermore, full-length variants can be now specifically selected based on the annotation of CAGE-tags and polyA signal and/or polyA sites, marking transcription initiation and termination sites, respectively. The retrieval can be carried out at gene, transcript, exon, protein or splice site level allowing the selection of data sets fulfilling one or more features settled by the user.

This content is being maintained by Graziano Pesole.

NAR Database Issue 2011
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tagsalternative splicing exons genetic databases genetic variation humans messenger rna protein isoforms protein sequence analysis proteins

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

BROPResource Content

http://brop.org/

Expression > Transcript Expression Analysis
Model Organisms > Microbes

The Bioinformatics Resource for Oral Pathogens (BROP) contains tools for genomics of oral pathogens including Genome Viewer, GOAL (genome wide ORF alignment), an oral pathogen microarray database, an entrez counter, oral pathogen specific BLAST, and a codon usage database.

NAR Web Server Issue 2005
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tagsbacteria bacterial capsules bacterial genes bacterial genome bacterial polysaccharides bacterial proteins biological evolution computational biology dna transposable elements fungal genome genetic databases genetic variation genomic islands genomics horizontal gene transfer integrases mouth oligonucleotide array sequence analysis open reading frames operon porphyromonas gingivalis sequence alignment streptococcus mutans transfer rna virulence virulence factors

CAPwebTool Content

http://bioinfo.curie.fr/CAPweb/

Expression > Transcript Expression Analysis

CGH array Analysis Platform (CAPweb) is a tool for storing, analyzing and visualizing CGH-array data.

NAR Web Server Issue 2006
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tagsalgorithms chromosome breakage chromosome mapping computational biology dna dna mutational analysis dna sequence analysis gene dosage genetic models genetic variation genomics humans in situ hybridization oligonucleotide array sequence analysis reproducibility of results sensitivity and specificity statistical models stochastic processes urinary bladder neoplasms

CPCTool Content

http://cpc.cbi.pku.edu.cn/programs/run_cpc.jsp

DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
RNA > Functional RNAs

CPC (Coding Potential Calculator) distinguishes protein-coding from non-coding RNAs based on the sequence features of the input transcripts.

NAR Web Server Issue 2007
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tagsanimals computational biology expressed sequence tags genetic code genetic transcription genetic variation genetic vectors messenger rna mice molecular sequence data nucleic acid databases protein biosynthesis proteins reproducibility of results rna

dbDNVDatabase Content

http://goods.ibms.sinica.edu.tw/DNVs/

DNA > Databases

The duplicated gene nucleotide variants database (dbDNV) (http://goods.ibms.sinica.edu.tw/DNVs/) promotes accurate variation annotation. Aside from the flat file download, users can explore the gene-related duplications and the associated DNVs by DGL and DNV searches, respectively. In addition, the dbDNV contains 304,110 DNV-coupled SNPs. From DNV-coupled SNP search, users observe which SNP records are also variants among duplicates.

This content is being maintained by wenlin.

NAR Database Issue 2011
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tagsduplicate genes genetic variation human genome humans molecular sequence annotation nucleic acid databases single nucleotide polymorphism

EnsemblDatabase Content

http://www.ensembl.org

DNA > Databases
Model Organisms > Databases

The Ensembl project provides high quality, integrated annotation on chordate and selected eukaryotic genomes within a consistent and accessible infrastructure. All supported species include comprehensive, evidence-based gene annotations and a selected set of genomes includes additional data focused on variation, comparative, evolutionary, functional and regulatory annotation. The most advanced resources are provided for key species including human, mouse, rat and zebrafish.

NAR Database Issue 2010NAR Database Issue 2011
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tagsanimals anopheles gambiae classification computational biology genetic databases genetic variation genome genomics humans mice molecular sequence annotation nucleic acid databases nucleic acid regulatory sequences open reading frames protein databases rats search engine single nucleotide polymorphism species specificity tertiary protein structure zebrafish

Ensembl Genome BrowserTool Content

http://www.ensembl.org/

DNA > Annotations
Human Genome > Annotations
Model Organisms > General Resources
Model Organisms > Other Organisms

Website, MySQL server and perl API access to software system which produces and maintains automatic annotation on eukaryotic genomes.

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tagsanimals bacterial genome base sequence cattle computational biology database management systems dna sequence analysis dogs fungal genome gene expression genetic databases genetic polymorphism genetic variation genome genomics human genome humans invertebrates mice nucleic acid databases nucleic acid regulatory sequences plant genome protein databases proteins rats reference standards rna sequence alignment species specificity synteny systems integration tertiary protein structure transcriptional regulatory elements

FINDbaseDatabase Content

http://www.findbase.org

Human Genome > Databases

Frequency of INherited Disorders database (FIND base) records frequencies of causative genetic variations worldwide. Database records include the population and ethnic group or geographical region, the disorder name and the related gene, accompanied by links to any related external resources and the genetic variation together with its frequency in that population. Other features include: (i) the systematic collection and thorough documentation of population/ethnic group-specific pharmacogenomic markers allele frequencies for markers in genes of pharmacogenomic interest from different classes of drug-metabolizing enzymes and transporters, representing 150 populations and ethnic groups worldwide; (ii) the development of new data querying and visualization tools in the expanded FINDbase data collection that facilitates querying of large data sets and visualizing the results; and (iii) the establishment of the first database journal, by affiliating FINDbase with Human Genomics and Proteomics journal.

NAR Database Issue 2011
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tagsethnic groups gene frequency genetic markers genetic variation humans inborn genetic diseases nucleic acid databases periodicals as topic pharmacogenetics

Geno2phenoTool Content

http://www.geno2pheno.org/cgi-bin/geno2pheno.pl

Model Organisms > Other Organisms

Geno2pheno takes as input an HIV-1 pol-gene DNA sequence and estimates phenotypic drug resistance to 17 antiretroviral drugs.

NAR Web Server Issue 2003
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tagsalgorithms anti-hiv agents artificial intelligence automated pattern recognition cluster analysis computational biology computer-assisted drug therapy computing methodologies decision trees disease susceptibility dna sequence analysis drug combinations factual databases gene expression profiling genetic models genetic polymorphism genetic variation genotype hiv hiv infections hiv-1 humans innate immunity molecular sequence data phenotype pol genes regression analysis reproducibility of results sensitivity and specificity statistical models viral dna viral drug resistance viral genome

GeSBAPTool Content

http://bioinfo.cipf.es/gesbap/

Expression > Gene Set Analysis
Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms

Gene Set based Analysis of Polymorphisms (GeSBAP) implements the gene set analysis to the evaluation of genome wide association studies. Gene set analysis is based on testing the association of modules of functionally related genes.

NAR Web Server Issue 2009
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tagsbiological processes breast neoplasms female genes genetic variation genome-wide association study humans single nucleotide polymorphism

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

GLUE, GLUE-IT, PEDEL, PEDEL-AA and DRIVeRTool Content

http://guinevere.otago.ac.nz/stats.html

DNA > Tools For the Bench

GLUE, PEDEL, and DRIVeR are tools for estimating completeness and diversity in randomized protein-encoding libraries; useful for guiding library design and for analyzing results. GLUE Including Translation (GLUE-IT) finds the expected amino acid completeness of libraries. PEDEL-AA calculates amino acid statistics for libraries generated by epPCR.

NAR Web Server Issue 2008
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tagsalgorithms chemical models codon computer simulation directed molecular evolution dna dna mutational analysis dna sequence analysis gene library genetic models genetic variation molecular evolution mutagenesis mutation peptide library point mutation polymerase chain reaction protein sequence analysis proteins statistical models

Gramene database in 2010Database Content

http://www.gramene.org

Model Organisms > Databases

The Gramene database has become a resource for major model and crop plants including Arabidopsis, Brachypodium, maize, sorghum, poplar and grape in addition to several species of rice. Gramene has an Ensembl genome browser and host a wide array of data sets including quantitative trait loci (QTL), metabolic pathways, genetic diversity, genes, proteins, germplasm, literature, ontologies and a fully-structured markers and sequences database integrated with genome browsers and maps from various published studies (genetic, physical, bin, etc.). In addition, Gramene now hosts a variety of web services including a Distributed Annotation Server (DAS), BLAST and a public MySQL database.

NAR Database Issue 2011
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tagschromosome mapping genetic databases genetic variation genomics metabolic networks and pathways plant genes plant genome plants quantitative trait loci synteny

HGNC: HUGO Gene Nomenclature CommitteeResource Content

http://www.genenames.org

DNA > DNA and Genomic Analysis
DNA > Sequence Retrieval and Submission
Human Genome > Other Resources
Protein > Sequence Retrieval

The HGNC approves a unique gene name and symbol for each known human gene. The HGNC Database is searchable and contains all approved symbols. For each symbol, if known, the database associates gene location, aliases, previous symbols and links out to sequence data and other databases.

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tagsanimals computational biology genes genetic databases genetic variation genomics human genome humans mice systems integration terminology as topic