AHM 2002

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AHM 2002

• Tutorial on Scientific Data Mediation
• Example 1

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Clusfavor
http//mbcr.bcm.tmc.edu/genepi/
wrap1
Accession Number
wrap2.xml
NCBI GeneBank
pwrap1
http//www.ncbi.nlm.nih.gov/
wrap2
Sequence to search
wrap3.xml
BLAST
pwrap2
http//www.ncbi.nlm.nih.gov/blast/
wrap3
The top match
wrap4.xml
http//transfac.gbf.de/cgi- bin/matSearch/matsearc
h.pl
MatInspector
pwrap3
Resulting sequences similarity scores
wrap4

• an external program to build a model or
• back to blast to find additional matches, or
• to clustal to determine a consensus sequence
  which is then sent to blast.

SCENARIO WORKFLOW
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CLUSFAVOR

• CLUSFAVOR- CLUSter and Factor Analysis with
  Varimax Orthogonal Rotation
• A standalone program whose output consists of
  several clusters of named sequences that have
  similar expression characteristics in the current
  experiment.
• GOAL Given a gene expression data, to end up
  with another set of related sequences from which
  to build a model.
• INPUT gene expression data
• OUTPUT collection of clustered cDNA fragments

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NCBI GeneBank

• GOAL Given the name (or, better, the accession
  number) of a cDNA string from the clusfavor
  results, do a name lookup in GenBank to obtain
  the cDNA sequence.
• INPUT The accession number or the name of a cDNA
  string
• OUTPUT cDNA sequence for the input cDNA string

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BLAST

• Basic Local Alignment Search Tool_ BLAST
• A set of similarity search programs designed to
  explore all of the available sequence databases
  regardless of whether the query is protein or
  DNA.
• INPUT Output cDNA sequence from GeneBank.
• OUPUT A set of similar sequences.

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MatInspector V2.2 based on TRANSFAC

• MatInspector - Matrix Inspector
• TRANSFAC - The Transcription Factor Database
• Search for potential transcription factor binding
  sites in your own sequences and detect consensus
  matches in nucleotide sequence data using the
  TRANSFAC 4.0 matrices.

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GENEBANK MEDIATION DEMO