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Links tagged with 'alleles'

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CanPredictTool Content

http://www.cgl.ucsf.edu/Research/genentech/canpredict/ [open in a new window]

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Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms
Protein > Sequence Features

CanPredict uses a combination of computational methods to predict whether specific sequence changes in a protein are likely to be cancer-associated mutations.

links directory index: 99
TitlePublication YearGoogle Scholar Citation Count
CanPredict: a computational tool for predicting cancer-associated missense mutations200747
Distinguishing cancer-associated missense mutations from common polymorphisms200752
NAR Web Server Issue 2007
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tagsalgorithms alleles amino acids computational biology expressed sequence tags genetic predisposition to disease humans missense mutation neoplasm dna neoplasms single nucleotide polymorphism tumor cell line

IKMCDatabase Content

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

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Model Organisms > Databases

The International Knockout Mouse Consortium (IKMC) database and web portal serves as the central public web site for IKMC data. Researchers can access up-to-date information on IKMC knockout vectors, ES cells and mice for specific genes, and follow links to the respective repositories from which corresponding IKMC products can be ordered. Researchers can also use the web site to nominate genes for targeting, or to indicate that targeting of a gene should receive high priority. The IKMC database provides data to, and features extensive interconnections with, other community databases.

This content is being maintained by damiansmedley.

links directory index: 16
TitlePublication YearGoogle Scholar Citation Count
BioMart as an integration solution for the International Knockout Mouse Consortium20112
The IKMC web portal: a central point of entry to data and resources from the International Knockout Mouse Consortium201114
NAR Database Issue 2011
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tagsalleles animals biomedical research database management systems embryonic stem cells gene knockout techniques gene targeting genetic databases genetic vectors genomics humans international cooperation knockout mice mice molecular sequence annotation phenotype societies

IMGT/3DstructureDatabase Content

http://www.imgt.org/3Dstructure-DB/ [open in a new window]

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Protein > Databases

IMGT/3Dstructure-DB is the three-dimensional (3D) structure database of IMGT, the international ImMunoGenetics information system for immunogenetics and immunoinformatics. IMGT/3Dstructure-DB contains 3D structures of immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility complex (MHC) proteins, antigen receptor/antigen complexes (IG/Ag, TR/peptide/MHC) of vertebrates; 3D structures of related proteins of the immune system (RPI) of vertebrates and invertebrates, belonging to the immunoglobulin and MHC superfamilies (IgSF and MhcSF, respectively) and found in complexes with IG, TR or MHC. IMGT/3Dstructure-DB data are annotated according to the IMGT criteria, using IMGT/DomainGapAlign, and based on the IMGT-ONTOLOGY concepts and axioms. IMGT/3Dstructure-DB provides IMGT gene and allele identification (CLASSIFICATION), region and domain delimitations (DESCRIPTION), amino acid positions according to the IMGT unique numbering (NUMEROTATION) that are used in IMGT/3Dstructure-DB cards, results of contact analysis and renumbered flat files. In its Web version, the IMGT/DomainGapAlign tool analyses amino acid sequences, per domain.

links directory index: 33
TitlePublication YearGoogle Scholar Citation Count
IMGT/3Dstructure-DB and IMGT/DomainGapAlign: a database and a tool for immunoglobulins or antibodies, T cell receptors, MHC, IgSF and MhcSF201033
NAR Database Issue 2010
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tagsalleles amino acid sequence amino acid sequence homology animals antigen receptors computational biology genetic databases humans immunoglobulins major histocompatibility complex molecular sequence data protein databases tertiary protein structure

IMGT/HLA databaseDatabase Content

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

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Human Genome > Databases

The IMGT/HLA database provides a searchable repository of highly curated HLA sequences. The naming of these HLA genes and alleles and their quality control is the responsibility of the WHO Nomenclature Committee for Factors of the HLA System. Through the work of the HLA Informatics Group and in collaboration with the European Bioinformatics Institute, we are able to provide public access to this data.

links directory index: 148
TitlePublication YearGoogle Scholar Citation Count
The IMGT/HLA database2011148
NAR Database Issue 2011
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tagsalleles hla antigens humans protein databases terminology as topic

IPDDatabase Content

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

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Human Genome > Databases

The Immuno Polymorphism Database (IPD) is a set of specialist databases related to the study of polymorphic genes in the immune system. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. IPD consists of four databases: IPD-KIR, contains the allelic sequences of Killer-cell Immunoglobulin-like Receptors, IPD-MHC, is a database of sequences of the Major Histocompatibility Complex of different species; IPD-human platelet antigens, alloantigens expressed only on platelets and IPD-ESTDAB, which provides access to the European Searchable Tumour cell-line database, a cell bank of immunologically characterised melanoma cell lines.

links directory index: 30
TitlePublication YearGoogle Scholar Citation Count
IPD--the Immuno Polymorphism Database201030
NAR Database Issue 2010
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tagsalleles animals base sequence computational biology genetic databases genetic polymorphism humans immune system immunogenetics molecular sequence data nucleic acid databases nucleic acid sequence homology protein databases

MLSTTool Content

http://www.mlst.net/ [open in a new window]

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DNA > Phylogeny Reconstruction
Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

MLST (Multi Locus Sequence Typing) is a nucleotide sequence based approach for the unambiguous characterisation of isolates of bacteria and other organisms using the sequences of internal fragments of seven house-keeping genes.

links directory index: 2035
TitlePublication YearGoogle Scholar Citation Count
The multilocus sequence typing network: mlst.net200589
Molecular typing of bacteria directly from cerebrospinal fluid200043
Multilocus sequence typing: molecular typing of bacterial pathogens in an era of rapid DNA sequencing and the internet1999136
Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms19981767
NAR Web Server Issue 2005
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tagsalleles bacteria bacterial dna bacterial genes bacterial meningitis bacterial typing techniques cerebrospinal fluid cluster analysis dna sequence analysis evaluation studies as topic gene frequency humans meningococcal infections molecular sequence data mycological typing techniques neisseria meningitidis nucleic acid databases pneumococcal meningitis polymerase chain reaction serotyping streptococcus pneumoniae virulence

Mouse Genome Database (MGD)Database Content

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

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Model Organisms > Databases

The Mouse Genome Database (MGD) is the community model organism database for the laboratory mouse and the source for phenotype and functional annotations of mouse genes. MGD includes a complete catalog of mouse genes and genome features with integrated access to genetic, genomic and phenotypic information. MGD contains standardized descriptions of mouse phenotypes, associations between mouse models and human genetic diseases, extensive integration of DNA and protein sequence data, normalized representation of genome and genome variant information. Major improvements to the Mouse Genome Database include comprehensive update of genetic maps, implementation of new classification terms for genome features, development of a recombinase (cre) portal and inclusion of all alleles generated by the International Knockout Mouse Consortium (IKMC).

links directory index: 318
TitlePublication YearGoogle Scholar Citation Count
The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse20125
The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics201177
The Mouse Genome Database: enhancements and updates201038
MGD: the Mouse Genome Database2003198
NAR Database Issue 2010NAR Database Issue 2011
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tagsalgorithms alleles animal models animals chromosome mapping computational biology genetic databases genetic models genome genomics genotype integrases knockout mice mice mutant strains mice nucleic acid databases phenotype terminology as topic

MousebookDatabase Content

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

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Model Organisms > Databases

The MouseBook databases and web portal provide access to information about mutant mouse lines held as live or cryopreserved stocks at MRC Harwell. The MouseBook portal integrates curated information from the MRC Harwell stock resource, and other Harwell databases, with information from external data resources to provide value-added information. MouseBook can be searched either using an intuitive Google style free text search or using the Mammalian Phenotype (MP) ontology tree structure. Text searches can be on gene, allele, strain identifier (e.g. MGI ID) or phenotype term and are assisted by automatic recognition of term types and autocompletion of gene and allele names covered by the database.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
MouseBook: an integrated portal of mouse resources20103
NAR Database Issue 2010
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tagsalleles animals automation computational biology cryopreservation genetic databases mice mutation nucleic acid databases phenotype

NetMHC-3.0Tool Content

http://www.cbs.dtu.dk/services/NetMHC [open in a new window]

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Human Genome > Health and Disease
Protein > Molecular Dynamics and Docking

NetNHC-3.0 is a web server for the prediction of human, mouse or monkey MHC Class I-peptide binding. Predictions are made for peptides of 8-11 amino acid length using artificial neural networks and weight matrices.

links directory index: 64
TitlePublication YearGoogle Scholar Citation Count
NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11200864
NAR Web Server Issue 2008
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tagsalleles animals epitopes haplorhini histocompatibility antigens class i hla antigens humans mice peptides

nHLAPredTool Content

http://www.imtech.res.in/raghava/nhlapred [open in a new window]

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Protein > 3-D Structure Prediction
Protein > Domains and Motifs

A highly accurate method for predicting MHC Class I restricted T cell epitopes for a large number of MHC Class I alleles.

This content is being maintained by raghavagps.

links directory index: 35
TitlePublication YearGoogle Scholar Citation Count
A hybrid approach for predicting promiscuous MHC class I restricted T cell epitopes200735
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tagsalleles animals computational biology epitopes genetic databases histocompatibility antigens class i humans MHC class I mhc class i genes neural networks (computer) peptides prediction proteasome endopeptidase complex T cell t-lymphocyte epitopes

PolyBayesTool Content

http://bioinformatics.bc.edu/marthlab/PolyBayes [open in a new window]

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DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms

UNIX-based SNP discovery from redundant sequences; integrated with Phred/Phrap/Consed infrastructure (see DNA -- Contig Assembly); free for non-commercial use.

links directory index: 395
TitlePublication YearGoogle Scholar Citation Count
A general approach to single-nucleotide polymorphism discovery1999395
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tagsalgorithms alleles bayes theorem expressed sequence tags genetic techniques genetic variation human genome humans sequence alignment single nucleotide polymorphism statistical data interpretation

ProPred1Tool Content

http://www.imtech.res.in/raghava/propred1 [open in a new window]

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Protein > Domains and Motifs

The ProPred-I is an on-line service for identifying the MHC Class-I binding regions in antigens. It implements matrices for 47 MHC Class-I alleles, proteasomal and immunoproteasomal models. The main aim of this server is to help users in identifying the promiscuous regions.

This content is being maintained by raghavagps.

links directory index: 106
TitlePublication YearGoogle Scholar Citation Count
ProPred1: prediction of promiscuous MHC Class-I binding sites2003106
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tagsalleles antigen presentation antigens binding peptides binding sites cysteine endopeptidases histocompatibility antigens class i immunoproteasome cleavage site macromolecular substances major histocompatibility complex MHC I multienzyme complexes oligopeptides peptides prediction proteasome cleavage site proteasome endopeptidase complex protein binding protein databases protein sequence analysis

SBT Interface - dbMHCTool Content

http://www.ncbi.nlm.nih.gov/gv/mhc/sbt.cgi?cmd=main [open in a new window]

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DNA > Sequence Polymorphisms
Human Genome > Other Resources
Human Genome > Sequence Polymorphisms
Protein > Networks & Interactions, Pathways and Enzymes

The SBT (Sequencing-based typing) interface is a tool accompanying the NCBI's Major Histocompatibility Complex database (dbMHC). It identifies the allelic composition of sequence-based typing (SBT) results of cDNA or genomic sequences. Samples are compared with databases containing all known alleles for several human leukocyte antigen (HLA) and killer cell immunoglobulin-like receptors (KIR) loci. An interactive sequence viewer allows inspection of the alignments.

links directory index: 11
TitlePublication YearGoogle Scholar Citation Count
The sequencing-based typing tool of dbMHC: typing highly polymorphic gene sequences200411
NAR Web Server Issue 2004
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tagsalgorithms alleles dna fingerprinting dna sequence analysis genetic polymorphism hla antigens immunologic receptors kir receptors nucleic acid databases sequence alignment
setsNational Center for Biotechnology Information (NCBI)

SVMHCTool Content

http://www-abi.informatik.uni-tuebingen.de/Services/SVMHC/ [open in a new window]

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DNA > Sequence Polymorphisms
Human Genome > Other Resources
Human Genome > Sequence Polymorphisms
Protein > Networks & Interactions, Pathways and Enzymes

SVMHC is a server for prediction of MHC class I and class II binding peptides. SVMHC can be used to find likely binders in a protein sequence and to investigate the effects of single nucleotide polymorphisms on MHC-peptide binding.

links directory index: 242
TitlePublication YearGoogle Scholar Citation Count
SVMHC: a server for prediction of MHC-binding peptides200640
Prediction of MHC class I binding peptides, using SVMHC2002202
NAR Web Server Issue 2006
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tagsalleles animals artificial intelligence computational biology histocompatibility antigens histocompatibility antigens class i hla antigens humans mice peptides predictive value of tests protein binding protein databases protein sequence analysis sensitivity and specificity single nucleotide polymorphism t-lymphocyte epitopes

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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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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