Sequence Retrieval

Resources in this section include sequence retrieval programs such as BLAST, EMBOSS, and Entrez.

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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

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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external linksLink on Wikipedia

NAPPDatabase Content

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Nucleic Acid Phylogenetic Profile Database: classifies coding and non-coding sequences in a genome according to their pattern of conservation across other genomes.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
NAPP: the Nucleic Acid Phylogenetic Profile Database.20121

NONCODEDatabase Content

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Database of all kinds of noncoding RNAs (except tRNAs and rRNAs). NONCODE also provides an efficient search option, allowing recovery of sequence, related publications and other information.

This content is being maintained by ncfans.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
NONCODE v3.0: integrative annotation of long noncoding RNAs20121

PubCrawlerTool Content

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It goes to the library. You go to the pub; receive email alerts for current contents of PubMed and GenBank; e.g. use accession number of htg record as query to receive sequence updates (as the version number changes).

RSATTool Content

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Regulatory Sequence Analysis Tools (RSAT) detects regulatory signals in non-coding sequences; tools include sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. Tools may be accessed separately or connected to other tools. As well, the tools are available as web services for integration into programmatic work flows. New tools incorporated include an automated sequence retrieval from EnsEMBL, motif comparison and motif quality tools, and the capacity to process ChIP-sequence data.

Software.ncrna.orgTool Content

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A suite of tools for analyzing non-coding RNA sequences on the basis of their secondary structures. Tools include those for structural multiple sequence alignments, structural pairwise sequence alignments and structural motif finding.

links directory index: 2
TitlePublication YearGoogle Scholar Citation Count
Software.ncrna.org: web servers for analyses of RNA sequences20082

SortMeRNA : ribosomal RNA reads filter for metatranscriptomic dataaResource Content

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Filters ribosomal RNA reads from metatranscriptomic runs produced by next-generation sequencers. Handles large RNA databases and sorts out all fragments matching the database with high accuracy and specificity.

links directory index: not available
TitlePublication YearGoogle Scholar Citation Count

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