> Tag > Links tagged with 'genetic variation'

Links tagged with 'genetic variation'

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Found 35 links

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Align-mTool Content

http://bioinformatics.vub.ac.be/software/software.html [open in a new window]

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Sequence Comparison > Multiple Sequence Alignments

Align-m is an accurate and highly versatile multiple alignment program. It consists of 3 modules, S2P, P2P and P2M (see figure, manual), which can be used separately or consecutively to accomplish several tasks.

links directory index: 81
TitlePublication YearGoogle Scholar Citation Count
Align-m--a new algorithm for multiple alignment of highly divergent sequences200481
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tagsalgorithms amino acid sequence amino acid sequence homology genetic variation molecular sequence data protein sequence analysis proteins reproducibility of results sensitivity and specificity sequence alignment

ASPicDBDatabase Content

http://www.caspur.it/ASPicDB/ [open in a new window]

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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.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing20113
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 [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

CPCTool Content

http://cpc.cbi.pku.edu.cn/programs/run_cpc.jsp [open in a new window]

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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.

This content is being maintained by CPC.

links directory index: 41
TitlePublication YearGoogle Scholar Citation Count
CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine200741
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/ [open in a new window]

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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.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
dbDNV: a resource of duplicated gene nucleotide variants in human genome20113
NAR Database Issue 2011
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external linksLink on Wikipedia
tagsduplicate genes genetic variation human genome humans molecular sequence annotation nucleic acid databases single nucleotide polymorphism

FINDbaseDatabase Content

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

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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.

links directory index: 2
TitlePublication YearGoogle Scholar Citation Count
FINDbase: a worldwide database for genetic variation allele frequencies updated20112
NAR Database Issue 2011
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external linksLink on Wikipedia
tagsethnic groups gene frequency genetic markers genetic variation humans inborn genetic diseases nucleic acid databases periodicals as topic pharmacogenetics

genenames.orgDatabase Content

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

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Literature > Databases

genenames.org displays all approved nomenclature within Symbol Reports that contain data curated by HUGO Gene Nomenclature Committee (HGNC) editors and links to related genomic, phenotypic and proteomic information. New features include a new Quick Gene Search, a new List Search, an integrated HGNC BioMart and a new Statistics and Downloads facility.

This content is being maintained by HGNC.

links directory index: 296
TitlePublication YearGoogle Scholar Citation Count
genenames.org: the HGNC resources in 2011201136
The HGNC Database in 2008: a resource for the human genome2008125
Genew: the Human Gene Nomenclature Database, 2004 updates2004135
NAR Database Issue 2011
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external linksLink on Twitter Link on Wikipedia
tagsanimals computational biology gene symbols genes genetic databases genetic variation genomics human genome humans information storage and retrieval internet mice nomenclature phenotype proteomics software systems integration terminology as topic user-computer interface

Geno2phenoTool Content

http://www.geno2pheno.org/cgi-bin/geno2pheno.pl [open in a new window]

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Model Organisms > Other Organisms

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

links directory index: 363
TitlePublication YearGoogle Scholar Citation Count
Methods for optimizing antiviral combination therapies200342
Geno2pheno: Estimating phenotypic drug resistance from HIV-1 genotypes2003147
Diversity and complexity of HIV-1 drug resistance: a bioinformatics approach to predicting phenotype from genotype2002174
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/ [open in a new window]

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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.

links directory index: 23
TitlePublication YearGoogle Scholar Citation Count
Gene set-based analysis of polymorphisms: finding pathways or biological processes associated to traits in genome-wide association studies200923
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

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

http://guinevere.otago.ac.nz/stats.html [open in a new window]

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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.

links directory index: 122
TitlePublication YearGoogle Scholar Citation Count
GLUE-IT and PEDEL-AA: new programmes for analyzing protein diversity in randomized libraries200826
Statistics of protein library construction200528
User-friendly algorithms for estimating completeness and diversity in randomized protein-encoding libraries200368
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 [open in a new window]

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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.

links directory index: 25
TitlePublication YearGoogle Scholar Citation Count
Gramene database in 2010: updates and extensions201125
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

HGVbaseDatabase Content

http://www.hgvbaseg2p.org/index [open in a new window]

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DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms

Human Genome Variation database - curated; attempt to summarize all known sequence variations in the human genome, to facilitate research into how genotypes affect common diseases, drug responses, and other complex phenotypes.

links directory index: 124
TitlePublication YearGoogle Scholar Citation Count
HGVbase: a human sequence variation database emphasizing data quality and a broad spectrum of data sources2002124
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tagsbase sequence chromosome mapping database management systems gene frequency genetic variation human genome humans inborn genetic diseases nucleic acid databases single nucleotide polymorphism systems integration

ICGC Data PortalDatabase Content

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

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Human Genome > Databases
Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms

The International Cancer Genome Consortium (ICGC) is a collaborative effort to characterize genomic abnormalities in 50 different cancer types. Currently has data from 24 cancer projects. Open access data (eg. Somatic mutations, copy number alterations, structural rearrangements, gene expression, miRNAs). Easy to search and analyze data, construct queries across multiple data sets.

links directory index: 8
TitlePublication YearGoogle Scholar Citation Count
International Cancer Genome Consortium Data Portal--a one-stop shop for cancer genomics data20118
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tagsdatabase management systems factual databases gene expression profiling genetic variation genomics humans international cooperation neoplasms societies

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

JEvTraceTool Content

http://www.cmpharm.ucsf.edu/~marcinj/JEvTrace/ [open in a new window]

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Protein > 3-D Structure Comparison
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences

Jevtrace is a tool that combines multiple sequence alignments, phylogenetic, and structural data for identification of functional sites in proteins.

links directory index: 845
TitlePublication YearGoogle Scholar Citation Count
JEvTrace: refinement and variations of the evolutionary trace in JAVA200218
An evolutionary trace method defines binding surfaces common to protein families1996827
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tagsamino acid sequence amino acid sequence homology animals bacterial proteins binding sites carrier proteins conserved sequence dna-binding proteins factual databases genetic variation glucocorticoid receptors haemophilus influenzae humans molecular evolution molecular models molecular sequence data mutation phylogeny protein conformation proteins quaternary protein structure rats rna-binding proteins sequence alignment src homology domains streptococcus pneumoniae zinc fingers

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