1. Systems Biology Tools for working with BIND data
First & Last Name
February X, 2003
Systems Biology Tools for working with BIND data
CBW Bioinformatics Workshop
February 26th, Vancouver
Ian Donaldson
Blueprint Initiative
Lab 10.4
(c) 2003 CGDN

2. In the lab Tools for working with BIND data
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February X, 2003
In the lab
Tools for working with BIND data
Field-specific text-searching
Accession number searches
BIND BLAST
PreBIND
The Interaction viewer
FAST
BIND index
SeqHound
Lab 10.4
(c) 2003 CGDN

3. Text and accession number searching
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February X, 2003
Text and accession number searching
Lab 10.4
(c) 2003 CGDN

4. http://blueprint.org First & Last Name February X, 2003 Lab 10.4
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5. First & Last Name
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6. First & Last Name
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Lab 10.4
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7. First & Last Name
February X, 2003
Lab 10.4
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8. First & Last Name
February X, 2003
Lab 10.4
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9. First & Last Name
February X, 2003
Lab 10.4
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10. First & Last Name
February X, 2003
Lab 10.4
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11. First & Last Name
February X, 2003
Lab 10.4
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12. First & Last Name
February X, 2003
Lab 10.4
(c) 2003 CGDN

13. First & Last Name
February X, 2003
BIND BLAST
Lab 10.4
(c) 2003 CGDN

14. First & Last Name
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Lab 10.4
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15. First & Last Name
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Lab 10.4
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16. First & Last Name
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Lab 10.4
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17. First & Last Name
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Lab 10.4
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18. First & Last Name
February X, 2003
Lab 10.4
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19. First & Last Name
February X, 2003
Lab 10.4
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20. First & Last Name
February X, 2003
Lab 10.4
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21. First & Last Name
February X, 2003
Lab 10.4
(c) 2003 CGDN

22. First & Last Name
February X, 2003
PreBIND
Lab 10.4
(c) 2003 CGDN

23. First & Last Name
February X, 2003
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.
Lab 10.4
(c) 2003 CGDN

24. First & Last Name
February X, 2003
Lab 10.4
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25. First & Last Name
February X, 2003
Lab 10.4
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26. First & Last Name
February X, 2003
Lab 10.4
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27. First & Last Name
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Lab 10.4
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28. First & Last Name
February X, 2003
Lab 10.4
(c) 2003 CGDN

29. The BIND Index First & Last Name February X, 2003 Lab 10.4
(c) 2003 CGDN

30. First & Last Name
February X, 2003
The BIND Index contains selected fields for BIND records in plain-text, 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.
Lab 10.4
(c) 2003 CGDN

31. First & Last Name
February X, 2003
Lab 10.4
(c) 2003 CGDN

32. First & Last Name
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33. First & Last Name
February X, 2003
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34. First & Last Name
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Lab 10.4
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35. First & Last Name
February X, 2003
Lab 10.4
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36. First & Last Name
February X, 2003
Lab 10.4
(c) 2003 CGDN

37. SeqHound
Lab 10.4

38. First & Last Name
February X, 2003
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.
Lab 10.4
(c) 2003 CGDN

39. First & Last Name
February X, 2003
Lab 10.4
(c) 2003 CGDN

40. First & Last Name
February X, 2003
Lab 10.4
(c) 2003 CGDN

41. Application Programing Interface
What is SeqHound?
GenBank
MMDB
MedLine
BIND
Taxonomy, GO,
LocusLink, CDD
SeqHound
SeqHound Module
Database Interface
Application Programing Interface
Local Programmer
Web Interface
Remote Interface
Lab 10.4
Web user
Remote Programmer

42. 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 "SHoundFindAcc ";
$aa = SHoundFindAcc("CAA28783");
print "SHoundFini ";
$aa = SHoundFini();
Lab 10.4

43. First & Last Name
February X, 2003
Lab 10.4
(c) 2003 CGDN