Sequence Retrieval

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

Found 29 links

Displaying 15 links


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.

BLAST2SRSTool Content

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

cpnDBDatabase Content

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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.

links directory index: 73
TitlePublication YearGoogle Scholar Citation Count
cpnDB: a chaperonin sequence database200473

DASMIwebDatabase Content

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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.

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
user feedback
external linksLink on Wikipedia

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)

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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