Surfacing is a tool for the functional analysis of domainome/genome evolution.
Currently its main application is the Dollo parsimony based inference of ancestral domainomes and
the functional analysis of the corresponding domain gains and losses.
Surfacing is implemented in Java as part of the
forester libraries.
The following analysis on the evolutionary dynamics of eukaryotic domain repertoires (domainomes) was performed using this tool:
Zmasek CM and Godzik A (2011)
"Strong functional patterns in the evolution of eukaryotic genomes revealed by the reconstruction of ancestral protein domain repertoires"
Genome Biology, 12:R4
The minimal input is:
Current version: 2.002 (2010.07.27)
Source code is available at [forester] at sourceforge.net
java -Xmx2048m -cp path\to\forester.jar org.forester.application.surfacing <options>
Options:
-input=<file>: file containing paths to the HMMER3 hmmscan output files to be analyzed
-species_tree=<file>: species tree in phyloXML format (for example: » tol_116.xml)
-obo=<file>: the GO obo file
-p2g=<file>: the Pfam to GO mapping file
-cos=<file>: file containing individual (per Pfam-domain) cutoff values
-neg_dom_filter=<file>: file listing domains to be ignored (e.g. viral domains)
-out_dir=<directory name>: the output directory
-o=<name>: base for output file names
-e=<double>: E-value cutoff
-dufs: to not ignore DUFs (domains of unknown function) [default is to ignore DUFs]
-no_eo: to igore engulfed domains [default is not ignore engulfed domains]
-h: for help and more options
Example:
"java -Xmx2048m -cp \soft\forester.jar org.forester.application.surfacing
-p2g=pfam2go_2009_10_01.txt -dufs -cos=Pfam_240_GA1 -obo=gene_ontology_2009_11_10.1_2.obo -no_eo -neg_dom_filter=viral_domains.txt -input=paths_to_hmmscan_results.txt -out_dir=domain_analysis_results -o=genomes_12 -species_tree=tree_of_life.xml"
Christian M Zmasek
Sanford-Burnham Medical Research Institute | phylosoft -at- gmail -dot- com
Last updated 2011.01.17