Wednesday, June 13, 2007

DNA sequence retrieval and submission tools

BankIt

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

BioMart

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).

BLAST

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

EBI Tools

EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services EBI provides through Simple Object Access Protocol (SOAP) and other related web service technologies.

EMBOSS

Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.

GeneLynx


A portal to the human genome. Query by text or BLAST, to access heaps of info from primary and secondary databases of genomic resources, transcripts, protein sequences, function, associated diseases, homologs, ests.

GenomeNet

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)

HGNC: HUGO Gene Nomenclature Committee

The HGNC approves a unique gene name and symbol for each known human gene. The Human Gene Nomenclature Database (Genew) 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.

MRS

MRS is a biological data retrieval system that can be accessed over the web, or installed and used locally. MRS indexes several flat-file data sets for searching, including EMBL nucleotide, UniProt, PDB and KEGG. Searches can be performed globally, or on one or more flat file fields per data set.

NCBI Human DNA Reference Sequence

Downloadable human DNA reference sequence. Annotation of genes and other genomic features will be available for browsing when complete.

PubCrawler

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).

SAKURA

SAKURA is the DDBJ DNA Database Submission System.

Sequin

Desktop tool developed by the NCBI for editing, annotating and submitting DNA sequences to any of the three DNA sequence submission sites (DDBJ, EMBL or GenBank).

SRS


Sequence Retrieval System network browser for multiple molecular databases.

Swiss-Shop

Submit sequence, pattern or keywords to receive email alert when new sequences of interest appear in SwissProt.

WEBIN

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