> > Sequence Retrieval

Sequence Retrieval

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

RSS FeedCompact ViewList as XMLList as JSON

Found 9 links

Displaying 9 links

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
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
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
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
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.

downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
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.

downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
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
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagschromosomes dna sequence analysis gene components humans nucleic acid databases

PubCrawlerTool Content

http://pubcrawler.gen.tcd.ie/

DNA > Sequence Retrieval and Submission
Literature > Search Tools
Protein > Sequence Retrieval
RNA > Sequence Retrieval

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).

NAR Web Server Issue 2004
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagselectronic mail information services medline national library of medicine (u.s.) nucleic acid databases pubmed united states

Ribosomal Database ProjectDatabase Content

http://rdp.cme.msu.edu/

DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction
RNA > Functional RNAs
RNA > Sequence Retrieval

Highly curated database of aligned and annotated rRNA sequences with accompanying phylogenies; data available for download.

downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsanimals archaea archaeal rna bacteria bacterial rna eukaryotic cells nucleic acid databases phylogeny prokaryotic cells ribosomal rna rna sequence analysis sequence alignment

RSATTool Content

http://rsat.ccb.sickkids.ca/

DNA > DNA and Genomic Analysis
DNA > Sequence Retrieval and Submission
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
RNA > Motifs
RNA > Sequence Retrieval

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.

NAR Web Server Issue 2003NAR Web Server Issue 2008NAR Web Server Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tags5' flanking region algorithms binding sites computational biology dna sequence analysis dna-binding proteins fungal gene expression regulation fungal genes fungal genome genetic transcription genome genomics nucleic acid regulatory sequences oligodeoxyribonucleotides saccharomyces cerevisiae transcription factors transcriptional regulatory elements yeasts

Software.ncrna.orgTool Content

http://software.ncrna.org

RNA > Functional RNAs
RNA > Motifs
RNA > Sequence Retrieval
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments

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.

NAR Web Server Issue 2008
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsnucleic acid conformation rna sequence analysis sequence alignment untranslated rna

Tags associated with subcategory 'RNA/Sequence Retrieval'

sequence alignment nucleic acid databases dna sequence analysis humans sequence analysis genome animals systems integration rna sequence analysis genetic databases protein sequence analysis united states algorithms computational biology genomics national library of medicine (u.s.) yeasts transcriptional regulatory elements saccharomyces cerevisiae transcription factors nucleic acid regulatory sequences oligodeoxyribonucleotides expressed sequence tags nucleic acids medline genetic transcription sensitivity and specificity pubmed protein databases nucleotides proteins sequence homology information services fungal genes fungal genome gene components base sequence factual databases electronic mail molecular biology chromosomes europe amino acid sequence nucleic acid conformation 5' flanking region binding sites biotechnology bibliographic databases archaea archaeal rna data collection untranslated rna nucleic acid sequence homology dna-binding proteins sequence tagged sites fungal gene expression regulation National Center for Biotechnology Information (NCBI) mutation bacterial rna bacteria eukaryotic cells phylogeny ribosomal rna prokaryotic cells