> > Sequence Retrieval and Submission

Sequence Retrieval and Submission

This section contains links for sequence retrieval and submission. The resources include alignment, sequence analysis as well as visualization tools.

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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

BankItTool Content

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

DNA > Sequence Retrieval and Submission

Web-based submission of one or a few sequences to GenBank.

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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)

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)

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

GeConT 2Tool Content

http://gecont.ibt.unam.mx/cgi-bin/gecont/gecont.pl

DNA > Sequence Retrieval and Submission
Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

The Gene Context Tool (GeConT) is a visualization tool for viewing the genomic context of a gene or group of genes, and their orthologous relationships, within any of the fully sequenced bacterial genomes. Sequence retrieval is also possible.

NAR Web Server Issue 2008
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tagsbacteria bacterial genes bacterial genome bacterial proteins conserved sequence genomics tertiary protein structure

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

International Nucleotide Sequence Database CollaborationDatabase Content

http://www.insdc.org

DNA > Sequence Retrieval and Submission

International Nucleotide Sequence Database Collaboration (INSDC) public domain nucleotide sequence is captured, preserved and presented. The partners of this long-standing collaboration work closely together to provide data formats and conventions that enable consistent data submission to their databases and support regular data exchange around the globe. Clearly defined policy and governance in relation to free access to data and relationships with journal publishers have positioned INSDC databases as a key provider of the scientific record and a core foundation for the global bioinformatics data infrastructure. While growth in sequence data volumes comes no longer as a surprise to INSDC partners, the uptake of next-generation sequencing technology by mainstream science that we have witnessed in recent years brings a step-change to growth, necessarily making a clear mark on INSDC strategy. In this article, we introduce the INSDC, outline data growth patterns and comment on the challenges of increased growth.

NAR Database Issue 2011
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tagsinternational cooperation nucleic acid databases organizational policy

MartViewTool Content

http://www.biomart.org/biomart/martview/

DNA > Annotations
DNA > Sequence Retrieval and Submission
DNA > Structure and Sequence Feature Detection
Human Genome > Annotations
Protein > Sequence Retrieval

The Ensembl EnsMart Genome Browser (MartView) is a tool for data retrieval and data mining that integrates data from Ensembl. Through the web interface MartView allows you to apply a series of filters to create custom datasets which can be converted to several useful output formats.

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tagsanimals base sequence computational biology database management systems genes genetic databases humans mice molecular sequence data rats
setsBioMart

MIGenAS ToolkitTool Content

http://www.migenas.org/

DNA > Phylogeny Reconstruction
DNA > Sequence Retrieval and Submission
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Localization and Targeting
Protein > Phylogeny Reconstruction
Protein > Sequence Retrieval
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Max-Planck Integrated Gene Analysis System (MIGenAS) provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction. Users can also configure \"meta\"-tools as a pipeline of individual tools and intermediate filters.

NAR Web Server Issue 2006
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tagsanimals computational biology genetic databases humans mice sequence alignment sequence analysis systems integration

Tags associated with subcategory 'DNA/Sequence Retrieval and Submission'

genetic databases humans animals computational biology sequence alignment nucleic acid databases proteins genomics sequence analysis mice systems integration dna sequence analysis protein databases genome algorithms base sequence protein sequence analysis molecular sequence data rats amino acid sequence saccharomyces cerevisiae transcription factors yeasts transcriptional regulatory elements time factors database management systems oligodeoxyribonucleotides nucleic acid regulatory sequences expressed sequence tags transcription initiation site rna sequence analysis messenger rna human genome translational peptide chain initiation dna-binding proteins genetic transcription fungal genome fungal genes fungal gene expression regulation nucleotides genes genetic models factual databases computer simulation information systems nucleic acids japan sequence homology molecular biology united states pubmed sensitivity and specificity ligands information services proteome genetic promoter regions national library of medicine (u.s.) medline Ontario Institute for Cancer Research (OICR) protein binding controlled vocabulary nucleic acid sequence homology chromosome mapping phylogeny electronic mail BioMart biology gene expression profiling neoplasm antigens European Bioinformatics Institute (EBI) europe mutation oligonucleotide array sequence analysis type ii dna topoisomerases gene components chromosomes international cooperation untranslated rna reference standards exons pseudogenes organizational policy bacteria biotechnology bibliographic databases binding sites amino acid sequence homology 5' flanking region biological models genetic variation ploidies plant genome plant genes viruses plant chromosomes single nucleotide polymorphism triticum sequence tagged sites natural language processing documentation gene expression regulation