surfacing

Overview

Surfacing is a tool for the functional analysis of domainome/genome evolution. Currently its main application is the Dollo/Fitch parsimony based inference of ancestral domainomes/domain combinations and the functional analysis of the corresponding domain gains and losses.

Surfacing is implemented in Java as part of the forester libraries.

Example Studies

The following analysis on the evolutionary dynamics of eukaryotic domain repertoires (domainomes) was performed using this tool:

Zmasek CM and Godzik A (2012) "This Déjà Vu Feeling—Analysis of Multidomain Protein Evolution in Eukaryotic Genomes" PLOS Computational Biology, 8, e1002701
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

Download

- Most current version (might be unstable): forester.jar

Source code is available at GitHub: https://github.com/cmzmasek/forester
example input files

Usage

% java -Xmx2048m -cp path\to\forester.jar org.forester.application.surfacing <options>

Input

The minimal input is:

Complete domain sets of the genomes to be analyzed, as HMMER3 hmmscan output files (use tabular output with --tblout option).
A evolutionary tree establishing the relationship between the genomes in question, in phyloXML format (for example » tol_156.xml).
A GO obo file and a Pfam to GO mapping file.

Examples

Basic:

% surfacing -p2g=pfam2go_130621.txt -obo=gene_onotology_130621.obo -species_tree=tol_156.xml -no_eo -ie=0.1 -dufs -genomes=genomes.txt -out_dir=_out1 -o=o1

all required input files to run this example (together with the corresponding example output) can be downloaded » here (as zip file)

With sequence extraction:

% surfacing -p2g=pfam2go_130621.txt -obo=gene_onotology_130621.obo -species_tree=tol_156.xml -last -ignore_viral_ids -no_eo -ie=0.1 -dufs -genomes=genomes_all.txt -pos_filter=tf_1.txt -all_prot -all_prot_e=0.1 -out_dir=_tf1_e01_ape01 -o=tf1_e01_ape01

Options (mandatory options are in bold)

Last modified: 2020-05-06