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Sequence Retrieval System

SRS is a homogeneous interface to over 80 biological databases developed at EBI, including databases of sequences, pathways, transcription factors, and results from tools like BLAST and FASTA. It allows users to search databases and run alignment algorithms on results. Entrez is a molecular biology database and retrieval system developed by NCBI that indexes data from sources like GenBank, PubMed, and PDB. It provides views of gene and protein sequences. DBGET is the backbone of the Japanese GenomeNet service and is used to search and extract entries from molecular biology databases, while LinkDB computes links between entries across databases.

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Ayesha Khan
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1K views

Sequence Retrieval System

SRS is a homogeneous interface to over 80 biological databases developed at EBI, including databases of sequences, pathways, transcription factors, and results from tools like BLAST and FASTA. It allows users to search databases and run alignment algorithms on results. Entrez is a molecular biology database and retrieval system developed by NCBI that indexes data from sources like GenBank, PubMed, and PDB. It provides views of gene and protein sequences. DBGET is the backbone of the Japanese GenomeNet service and is used to search and extract entries from molecular biology databases, while LinkDB computes links between entries across databases.

Uploaded by

Ayesha Khan
Copyright
© © All Rights Reserved
Available Formats
Download as DOCX, PDF, TXT or read online on Scribd
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Sequence Retrieval System (SRS) :

 SRS is a homogeneous interface to over 80 biological databases that had been developed at
the European Bioinformatics Institute (EBI) at Hinxton, UK.
 It includes databases of sequences, metabolic pathways, transcription factors, application
results (like BLAST, SSEARCH, FASTA), protein 3-D structures, genomes, mappings,
mutations, and locus specific mutations.
 The web page listing all the databases contains a link to a description page about the
database including the date on which it was last updated. One or more of the databases is
selected to search before entering your query.
 After getting results, choose an alignment algorithm (like CLUSTALW, PHYLIP) enter
parameters, and run it.
 The SRS is highly recommended for use.

Entrez:

 Entrez is a molecular biology database and retrieval system.


 Developed by the National Center for Biotechnology information (NCBI).
 It is entry point for exploring distinct but integrated databases. Of the three text-based
database systems, Entrez is the easiest to use, but also offers more limited information to
search.
 Entrez is both an indexing and retrieval system having data from various sources for
biomedical research.
 Entrez is composed of nucleotide sequences from PDB and GenBank, protein sequences
from SWISS-PROT, translated GenBank, PIR, PRF, PDB and associated abstracts and
citations from PubMed.
 The Entrez system can provide views of gene and protein sequences and chromosome maps.

DBGET:
 The integrated database retrieval system DBGET/LinkDB is the backbone of the Japanese
GenomeNet service.
 DBGET is used to search and extract entries from a wide range of molecular biology
databases, while LinkDB is used to search and compute links between entries in different
databases.
 The WWW version of DBGET/LinkDB at GenomeNet is integrated with other search tools,
such as BLAST, FASTA and MOTIF, and with local helper applications, such as RasMol. 

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