> > Sequence Retrieval

Sequence Retrieval

These resources include links to protein sequence retrieval tools including BLAST, EMBOSS, Entrez, and SRS.

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Found 28 links

Displaying 15 links

AliasServerDatabase Content

http://cbi.labri.fr/outils/alias/

DNA > Sequence Retrieval and Submission
Protein > Sequence Retrieval

A tool for converting identifiers in which multiple aliases are used to refer to sequences. Also available as a stand-alone tool.

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tagsalgorithms controlled vocabulary database management systems documentation natural language processing protein databases protein sequence analysis proteins sequence alignment

BioMartTool Content

http://biomart.org

DNA > Sequence Retrieval and Submission
DNA > Structure and Sequence Feature Detection
Protein > Interactions, Pathways, Enzymes
Protein > Sequence Retrieval
RNA > Databases

BioMart is an interactive data integration system facilitating large-scale data queries. It can be installed and used in-house, or with one of the existing data sources to which is has already been applied (ie. UniProt, Ensembl).

NAR Web Server Issue 2009
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tagsbiology genetic databases
setsBioMart Ontario Institute for Cancer Research (OICR)

BioverseTool Content

http://bioverse.compbio.washington.edu/

DNA > Annotations
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Annotation and Function
Protein > Sequence Comparison
Protein > Sequence Retrieval

Bioverse is a system that uses computational techniques to facilitate exploring the relationships between molecular, genomic, proteomic, systems and organismal information.

NAR Web Server Issue 2005NAR Web Server Issue 2003
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tagsamino acid sequence homology biological models chromosome mapping computer simulation energy metabolism gene expression profiling gene expression regulation molecular models protein conformation protein interaction mapping protein sequence analysis proteins proteome proteomics signal transduction

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)

BLAST2SRSTool Content

http://blast2srs.embl.de/

Protein > Sequence Retrieval
Sequence Comparison > Similarity Searching

BLAST2SRS (Sequence Retrieval System) is a tool to retrieve protein sequences using similarity (BLAST) and keyword searches.

NAR Web Server Issue 2003
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tagsamino acid sequence homology animals humans protein databases

Cascade PSI-BlastDatabase Content

http://crick.mbu.iisc.ernet.in/~CASCADE/CascadeBlast.html

Protein > Domains and Motifs
Protein > Sequence Retrieval
Sequence Comparison > Similarity Searching

Cascade PSI-BLAST detects distant protein similarities using a cascade search protocol where PSI-BLAST searches are carried out on each hit, until no new hits are found in the selected database (SwissProt, SCOP, or Pfam).

NAR Web Server Issue 2006
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tagsamino acid sequence amino acid sequence homology molecular models molecular sequence data protein conformation protein databases protein folding protein sequence analysis proteins sequence alignment tertiary protein structure

cpnDBDatabase Content

http://www.cpndb.ca/cpnDB/home.php

DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction
Protein > Sequence Data
Protein > Sequence Retrieval

cpnDB is a curated collection of chaperonin sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic and microbial ecology studies. The database contains all available sequences for both group I and group II chaperonins. cpnDB is built and maintained with open source tools.

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tagsanimals bacteria base sequence chaperonin 60 computational biology genetic databases molecular sequence data nucleic acid sequence homology

DASMIwebDatabase Content

http://www.dasmiweb.de

Protein > Interactions, Pathways, Enzymes
Protein > Sequence Retrieval

The DASMIweb server allows integration, analysis and quantitative assessment of distributed sources of protein and domain interactions. Users can query numerous sources simultaneously, which can then be configured and can support incorporation of user data.

NAR Web Server Issue 2009
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tagsonline systems protein interaction domains and motifs protein interaction mapping systems integration

EBI ToolsTool Content

http://www.ebi.ac.uk/Tools/webservices/

Computer Related > Web Services
DNA > Sequence Retrieval and Submission
Education > Directories and Portals
Literature > Search Tools
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies.

NAR Web Server Issue 2005NAR Web Server Issue 2007NAR Web Server Issue 2009
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tagsbibliographic databases biotechnology computational biology europe genetic databases nucleic acids protein sequence analysis proteins sequence alignment sequence analysis sequence homology systems integration

EMBOSSTool Content

http://emboss.bioinformatics.nl/

DNA > DNA and Genomic Analysis
DNA > Sequence Retrieval and Submission
DNA > Structure and Sequence Feature Detection
DNA > Tools For the Bench
Protein > Biochemical Features
Protein > Do-it-all Tools for Protein
Protein > Presentation and Format
Protein > Sequence Features
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.

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tagsmolecular biology sequence alignment

EntrezDatabase Content

http://www.ncbi.nlm.nih.gov/Entrez/index.html

DNA > Sequence Retrieval and Submission
Protein > Sequence Data
Protein > Sequence Retrieval
RNA > Sequence Retrieval

NCBI information retrieval system, including GenBank, MMDB (structures), genomes, population sets, OMIM, taxonomy and PubMed.

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tagsanimals data collection dna sequence analysis expressed sequence tags genomics humans nucleic acid databases sequence tagged sites

FeatureExtractTool Content

http://www.cbs.dtu.dk/services/FeatureExtract/

DNA > Annotations
DNA > Sequence Retrieval and Submission
Human Genome > Annotations
Protein > Sequence Retrieval
RNA > Sequence Retrieval

The FeatureExtract server extracts sequence and feature annotations, such as intron/exon structure, from GenBank entries and other GenBank format files.

NAR Web Server Issue 2005
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tagschromosomes dna sequence analysis gene components humans nucleic acid databases

Gene Set BuilderTool Content

http://www.cisreg.ca/gsb/

DNA > Sequence Retrieval and Submission
Human Genome > Annotations
Human Genome > Other Resources
Model Organisms > General Resources
Protein > Sequence Retrieval

Gene Set Builder is a database-driven, web-based tool designed to help researchers compile, store, export, and share sets of genes. This application supports the 17 eukaryotic genomes found in version 32 of the Ensembl database, which includes species from yeast to human. User-created information such as sets and customized annotations are stored and can be shared to facilitate easy access. Gene sets stored in the system can be exported in a variety of output formats - as lists of identifiers, in tables, or as sequences.

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tagscomputational biology database management systems factual databases fungal genes gene expression regulation genetic databases genome genomics humans programming languages

GenomeNetTool Content

http://www.genome.ad.jp/

DNA > Sequence Retrieval and Submission
Human Genome > Other Resources
Protein > Interactions, Pathways, Enzymes
Protein > Sequence Retrieval

Network of database and computational resources including KEGG (pathways, interactions, etc.) and DBGET/LinkDB (an integrated database retrieval system). It also hosts several web-based tools for sequence analysis (ie. Blast, Motif, Clustal W)

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tagsamino acid sequence animals biological models computer simulation factual databases genetic models genome humans information systems japan ligands molecular biology molecular sequence data protein binding proteome

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

Tags associated with subcategory 'Protein/Sequence Retrieval'

genetic databases humans animals proteins protein sequence analysis protein databases sequence alignment computational biology nucleic acid databases systems integration mice sequence analysis amino acid sequence algorithms genomics amino acid sequence homology molecular sequence data expressed sequence tags rats information services nucleotides dna sequence analysis genes proteome terminology as topic publications molecular models protein conformation database management systems tertiary protein structure protein folding sequence homology japan genetic models factual databases genome information systems ligands nucleic acids molecular biology computer simulation united states protein binding sensitivity and specificity Ontario Institute for Cancer Research (OICR) medline pubmed signal transduction national library of medicine (u.s.) protein interaction mapping proteomics oligonucleotide array sequence analysis neoplasm antigens dna-binding proteins type ii dna topoisomerases mutation biological models European Bioinformatics Institute (EBI) europe National Center for Biotechnology Information (NCBI) chromosome mapping phylogeny biotechnology bibliographic databases amino acid motifs online systems chromosomes gene components electronic mail biology BioMart artificial intelligence genetic variation human genome controlled vocabulary natural language processing documentation nucleic acid sequence homology time factors sequence tagged sites gene expression regulation gene expression profiling energy metabolism programming languages fungal genes sequence deletion secondary protein structure polymerase chain reaction oligonucleotides x-ray crystallography protein interaction domains and motifs chaperonin 60 base sequence bacteria data collection