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

In the lab Tools for working with BIND data First & Last Name 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

Text and accession number searching First & Last Name February X, 2003 Text and accession number searching Lab 10.4 (c) 2003 CGDN

http://blueprint.org First & Last Name February X, 2003 Lab 10.4 (c) 2003 CGDN

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

SeqHound Lab 10.4

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

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

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

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

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

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