GT
PHYLOGENETIC PROFILING
State of the problem
http://bioinfo.cacs.louisiana.edu/profile/
A tool for building phylogenetic profiles of a gene against a set of archaea, bacteria and eukaryotes
Phylogenetic profiling creates a binary vector where 1 denotes the presence of the gene in the genome, and 0 – the absence.
Proposed extension
Rebuild phylogenetic profiles using more genomes than there were previously available
Given a sequence (protein), show profile “on the fly” and predict its function
implementation
I focused on the 2nd extension for processing the sequence “on the fly”
Using NCBI Blastp online tool, I aligned the sequence against other genes from the system
I crawled the website and parsed the good results, with query cover (> 70%)
The genes are given by accession number / gi – from any of these ids I found the taxonomy number
The taxonomy number would represent the genome
Profiling: 1 for the taxonomies where a matching gene was found, 0 for all the others
I save all the taxonomies and their mapping to the domain {EUK, ARCH, BACT} in a database
The new profile will not be saved in the database
Demo with input a giardia gene
RESULT
This Giardia gene actually matches with genes from all three domains
To be continued
Improve the speed by running local Blast instead of online
Functional prediction – the function might be assumed identical to the best matched gene
Re-build the previous phylogenetic profiles using more genomes & local BLAST
Questions?