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Links tagged with 'mutation'

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Found 51 links

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BLASTTool Content

http://www.ncbi.nlm.nih.gov/BLAST/

DNA > Gene Prediction
DNA > Sequence Retrieval and Submission
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Similarity Searching

Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

NAR Web Server Issue 2004NAR Web Server Issue 2006NAR Web Server Issue 2008
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tagsalgorithms amino acid sequence base sequence factual databases genetic databases genome humans mutation national library of medicine (u.s.) nucleic acid databases nucleic acid sequence homology nucleotides protein databases protein sequence analysis sensitivity and specificity sequence alignment sequence analysis systems integration united states
setsNational Center for Biotechnology Information (NCBI)

CCRXPTool Content

http://ccrxp.netasa.org

Protein > 3-D Structural Features
Protein > Sequence Features

A tool for the detection of conserved residue clusters from an input PDB file. Structural properties of each residue, such as solvent accessibility (ASA), secondary structure, conservation score etc. and the conserved residue clusters are also computed.

This content is being maintained by shandar.

NAR Web Server Issue 2010
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tagsclustered residues consensus sequence conservation score dna-binding proteins hot spots interface multiprotein complexes mutation proteins rna-binding proteins solvent accessibility

corRnaTool Content

http://corrna.cs.mcgill.ca

RNA > Functional RNAs

corRna is a web server for predicting the multiple point deleterious mutations in structural RNAs. Users can apply search heuristics to improve the quality of the predictions.

NAR Web Server Issue 2011
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tagsalgorithms mutagenesis mutation nucleic acid conformation rna

COSMICDatabase Content

http://www.sanger.ac.uk/genetics/CGP/cosmic/

DNA > Databases
Human Genome > Databases

COSMIC curates comprehensive information on somatic mutations in human cancer. Release v48 (July 2010) describes over 136,000 coding mutations in almost 542,000 tumour samples; of the 18,490 genes documented, 4803 (26%) have one or more mutations. Full scientific literature curations are available on 83 major cancer genes and 49 fusion gene pairs. Biomart allows more automated data mining and integration with other biological databases. Annotation of genomic features has become a significant focus. COSMIC integrates many diverse types of mutation information and is making much closer links with Ensembl and other data resources.

NAR Database Issue 2010NAR Database Issue 2011
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tagscomputational biology data mining genetic databases human genome humans mutation neoplasms nucleic acid databases protein databases search engine tumor cell line

DBASS3 and DBASS5Database Content

http://www.dbass.org.uk/

DNA > Databases

DBASS3 and DBASS5 provide comprehensive repositories of new exon boundaries that were induced by pathogenic mutations in human disease genes. Aberrant 5'- and 3'-splice sites were activated either by mutations in the consensus sequences of natural exon-intron junctions (cryptic sites) or elsewhere ('de novo' sites). DBASS3 and DBASS5 data can be searched by disease phenotype, gene, mutation, location of aberrant splice sites in introns and exons and their distance from authentic counterparts, by bibliographic references and by the splice-site strength estimated with several prediction algorithms. The user can also retrieve reference sequences of both aberrant and authentic splice sites with the underlying mutation.

NAR Database Issue 2011
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tagsdisease humans mutation nucleic acid databases rna splice sites terminology as topic

DIMA 3.0Database Content

http://webclu.bio.wzw.tum.de/dima

Protein > Databases

Domain Interaction MAp (DIMA) is a database of predicted and known interactions between protein domains. It integrates 5807 structurally known interactions imported from the iPfam and 3did databases and 46,900 domain interactions predicted by four computational methods: domain phylogenetic profiling, domain pair exclusion algorithm correlated mutations and domain interaction prediction in a discriminative way. Additionally predictions are filtered to exclude those domain pairs that are reported as non-interacting by the Negatome database. The DIMA Web site allows to calculate domain interaction networks either for a domain of interest or for entire organisms, and to explore them interactively using the Flash-based Cytoscape Web software.

NAR Database Issue 2011
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tagsmutation protein databases protein interaction domains and motifs protein interaction mapping

DrugScorePPITool Content

http://cpclab.uni-duesseldorf.de/dsppi

Protein > Interactions, Pathways, Enzymes
Protein > Sequence Features

DrugScorePPI web server performs alanine scanning within a given protein-protein complex in silico. Useful for guiding biological experiments and in the development of protein-protein interaction modulators.

NAR Web Server Issue 2010
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tagsalanine multiprotein complexes mutation protein interaction mapping ral gtp-binding proteins ral guanine nucleotide exchange factor

EpiToolKitTool Content

http://www.epitoolkit.org

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

A suite of tools for immunological research. EpiToolKit offers a variety of prediction methods that may be run simultaneously for predicting MHC Class I and II ligands, and minor histocompatibility antigens. The influence of sequence polymorphisms or mutations on potential T-cell epitopes may also be examined.

NAR Web Server Issue 2008
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tagsacetaminophen child computational biology dosage forms drug packaging france genetic polymorphism histocompatibility antigens humans ligands mutation neoplasm antigens non-narcotic analgesics oral administration peptides poison control centers poisoning protein sequence analysis t-lymphocyte epitopes

ET Report MakerTool Content

http://mammoth.bcm.tmc.edu/report_maker/

Protein > 3-D Structural Features
Protein > Annotation and Function

Evolutionary trace (ET) report maker pools information from different sources including databases and on-the-fly multiple sequence analysis to produce a pdf formatted document as output. The emphasis is on prediction of functional sites of proteins.

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tagsalgorithms animals biological evolution computational biology humans molecular evolution mutation protein databases proteins statistical models

FlyBaseDatabase Content

http://flybase.bio.indiana.edu/

Model Organisms > Fly

FlyBase is a database of genetic and molecular data for Drosophila. FlyBase includes data on all species from the family Drosophilidae; the primary species represented is Drosophila melanogaster.

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tagsanimals bibliography as topic california chromosome mapping computational biology drosophila drosophila melanogaster drosophila proteins europe factual databases gene expression gene library genetic databases genetic models genetic transcription genome insect genes mutation phenotype publishing research

FOLD-RATETool Content

http://psfs.cbrc.jp/fold-rate/

Protein > Molecular Dynamics and Docking

FOLD-RATE predicts the folding rates of proteins from their amino acid sequences.

NAR Web Server Issue 2006
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tagsamino acid sequence amino acids binding sites chemical models kinetics linear models molecular models mutation protein conformation protein folding protein sequence analysis protein structural homology proteins secondary protein structure solvents statistical models statistics as topic tertiary protein structure thermodynamics

FoldXTool Content

http://foldx.embl.de/

Protein > 3-D Structure Prediction
Protein > Molecular Dynamics and Docking

FOLD-X is a program for calculating the folding energies of proteins and for calculating the effect of a point mutation on the stability of a protein.

NAR Web Server Issue 2005
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tagsmolecular structure mutation nucleic acid conformation protein conformation protein databases protein folding proteins single nucleotide polymorphism

GenePath2Tool Content

http://www.genepath.org/genepath2

Protein > Interactions, Pathways, Enzymes

GenePath is a tool for automated construction of genetic networks and proposal of genetic experiments from mutant data.

NAR Web Server Issue 2005
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tagsanimals artificial intelligence caenorhabditis elegans computational biology dictyostelium dna dna mutational analysis dna sequence analysis expert systems gene expression regulation genes genetic epistasis genetic models genomics humans knowledge larva mutation neural networks (computer) research single-blind method

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

GoGeneTool Content

http://gopubmed.biotec.tu-dresden.de/gogene

DNA > Annotations
Literature > Text Mining and Semantics

GoGene performs high-throughput text mining to complement annotation of genes. GoGene supports search for genes in PubMed, EntrezGene and BLAST.

NAR Web Server Issue 2009
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tagsanimals bone resorption controlled vocabulary gene expression profiling genes hepatoerythropoietic porphyria humans mice mutation oligonucleotide array sequence analysis osteoporosis pancreatic neoplasms pubmed rats