AHM 2002 Tutorial on Scientific Data Mediation Example 1.

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Presentation transcript:

AHM 2002 Tutorial on Scientific Data Mediation Example 1

Clusfavor NCBI: GeneBank BLAST MatInspector Accession Number Sequence to search wrap1 1)an external program to build a model or 2)back to blast to find additional matches, or 3)to clustal to determine a consensus sequence which is then sent to blast. wrap2 pwrap1 pwrap2 wrap3 pwrap3 wrap4 Resulting sequences & similarity scores The top match : wrap2.xml : wrap3.xml : wrap4.xml bin/matSearch/matsearch.pl SCENARIO WORKFLOW

CLUSFAVOR CLUSFAVOR- CLUSter and Factor Analysis with Varimax Orthogonal RotationCLUSFAVOR 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

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.GenBank INPUT: The accession number or the name of a cDNA string OUTPUT: cDNA sequence for the input cDNA string

BLAST Basic Local Alignment Search Tool_ BLASTBLAST 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.

MatInspector V2.2MatInspector V2.2 based on TRANSFAC 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.

GENEBANK MEDIATION DEMO