Sequence Searching & Retrieval

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Programs available locally are shown in pink.  Links to their parent/ official mirror sites are given below:
 
LookUp  -  as part of GCG package only.
LookUp identifies sequence database entries by name,
accession number, author, organism, keyword, title, 
reference, feature, definition, length, or date.  The output 
is a list of sequences.

 
StringSearch   -  as part of GCG package only.
StringSearch identifies sequences by searching for 
character patterns such as "globin" or "human" in the 
sequence documentation.

 
  Names  - as part of GCG package only.
Names identifies GCG data files and sequence entries by 
name. It can show you what set of sequences is implied by 
any sequence specification.

 
Fetch  -  as part of GCG package only.
Fetch copies GCG sequences or data files from the GCG 
database into your directory or displays them on your 
terminal screen.

 
FASTA
FastA does a Pearson and Lipman search for similarity 
between a query sequence and a group of sequences of 
the same type (nucleic acid or protein).
See also:
http://www2.ebi.ac.uk/fasta3/

 
BLAST
BLAST searches for sequences similar to a query sequence.
The query and the database searched can be either peptide 
or nucleic acid in any combination.  BLAST can search 
databases on your own computer or databases maintained at 
the National Center for Biotechnology Information (NCBI) in 
Bethesda, Maryland, USA.
See also:
http://www.ncbi.nlm.nih.gov/BLAST/

 
Protein Sequence Search Tool [PSST 1.0]
A web-based search tool, PSST has been developed to retrieve the user 
input query from the single letter amino acid code input file 
"pdb_seqres.txt", obtained from the Protein Data Bank.  The search tool
consists of the following four modules:
(a)    Amino acid composition and molecular weight
(b)    Molecular Weight Range
(c)    Pattern Matching (Identity)
(d)    Pattern Matching  (Similarity)
Depending upon the search category, the search tool will search the 
protein sequence database (updated every week from the Protein Data 
Bank , USA) resided in our Bioinformatics Server and will display the
related search results to the client browser.  Further, developmental
work on this search tool is in progress.

 
*1*DBGET :-
Integrated Database Retrieval System (w/ diagram links) at
GenomeNet, Japan

 
*3*DDBJ:-
DNA Database of Japan at National Institute of Genetics, Japan

 
ENTREZ  :-
Integrated search system for sequence, structure and Medline databases
at the National Center for Biotechnology Information, USA

 
SRSWWW :-
Network Browser for Databanks in Molecular Biology at
EMBL-Heidelberg