Transcript Information Encoding in Biological Molecules: DNA and

Systems Biology
Tools for working with BIND data
CBW Bioinformatics Workshop
February 26th, Vancouver
Ian Donaldson
Blueprint Initiative
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In the lab
• Tools for working with BIND data
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Field-specific text-searching
Accession number searches
BIND BLAST
PreBIND
The Interaction viewer
FAST
BIND index
SeqHound
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Text and accession number
searching
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http://blueprint.org
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BIND BLAST
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PreBIND
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PreBIND is a literature search tool that helps users
find interaction data in abstracts for their protein of
interest.
Currently available for yeast, human and mouse
proteins.
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The BIND Index
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The BIND Index contains selected fields for BIND records in plaintext, tab-delimited format.
ftp://ftp.blueprint.org/pub/BIND/current/bindflatfiles/bindindex/
These files may be used to locate BIND records that describe a given
biomolecule. BIND records contain many other fields than those
listed in these indices. Complete BIND records are available in XML
or ASN.1 format from ftp://ftp.bind.ca/pub/BIND/data.
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SeqHound
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SeqHound is a bioinformatics application programming
platform. A remote application programming interface (API) in
C, C++, PERL or Java is available.
This API will give you access to a database of biological
sequences and structures. Seqhound also stores additional
information related to each of these sequences. This includes
links to Genome Ontology descriptions, Medline abstracts,
taxon descriptions, associated structures, redundant
sequences, sequence neighbours, conserved domains,
database cross-references, Online Mendelian Inheritance in
Man identifiers, LocusLink identifiers and complete genomes.
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What is SeqHound?
GenBank
Taxonomy, GO,
LocusLink, CDD
MMDB
MedLine
BIND
SeqHound
SeqHound Module
Database Interface
Application Programing Interface
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Web Interface
Remote Interface
Local Programmer
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Remote Programmer
A sample seqhound program using the Perl API
#!/usr/bin/perl -w
use strict;
use SeqHound;
print "Starting Program\n";
print "SHoundInit ";
my $aa = SHoundInit("TRUE", "myapp");
print "$aa\n";
print "SHoundIsInited ";
$aa = SHoundIsInited();
print "$aa\n";
print "SHoundFindAcc ";
$aa = SHoundFindAcc("CAA28783");
print "$aa\n";
print "SHoundFini ";
$aa = SHoundFini();
print "$aa\n";
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