Sequence Retrieval and Submission

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

Found 31 links

Displaying 15 links

BankItTool Content

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

links directory index: not available
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BLASTTool Content

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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. A new BLAST report allows faster loading of alignments, has navigation aids and has improved usability.

BWT-SWTool Content

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BWT-SW is a local alignment tool for searching nucleotide sequences. It performs the same function as BLASTn, the BLAST program for finding regions of local similarity between nucleotide sequences. While BLAST is an approximation of the Smith-Waterman local alignment algorithm and may miss significant alignments (see BLAST Sensitivity), BWT-SW finds all local alignments.

links directory index: 47
TitlePublication YearGoogle Scholar Citation Count
Compressed indexing and local alignment of DNA200847

CDSbankResource Content

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CDSbank filters/expands/formats/labels large protein(-coding) sequence sets with full access to genbank feature annotation and taxonomy. Its input is just a list of protein identifiers or sequences, its output can be both protein and/or DNA sequences with informative labels. CDSbank can also 1) add synonymous CDS, 2) cluster sequences by taxonomy, 3) reject partial or ambiguous sequences, 4) select a best representative for each cluster to reduce redundancy.

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EBI ToolsTool Content

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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. Example tools include those to compute sequence similarity searches, pairwise/multiple sequence alignment and protein functional analysis.

EntrezDatabase Content

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

links directory index: 412
TitlePublication YearGoogle Scholar Citation Count
GenBank2003412
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GeConT 2Tool Content

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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.

Gene Set BuilderTool Content

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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.

GenomeNetTool Content

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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)

International Nucleotide Sequence Database CollaborationDatabase Content

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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.

links directory index: 15
TitlePublication YearGoogle Scholar Citation Count
The International Nucleotide Sequence Database Collaboration201115

MartViewTool Content

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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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