fathmm

This is the source code for the Functional Analysis through Hidden Markov Models software and server (http://fathmm.biocompute.org.uk).

General Requirements

You will need the following packages installed on your system:

• MySQL
• Python & Python MySQLdb (tested with Python 2.6/2.7)

Setup:

• Our pre-computed database can be found at http://fathmm.biocompute.org.uk/database/fathmm.v2.3.SQL.gz (instructions on how to create/upload the database can be found at http://fathmm.biocompute.org.uk/database/INSTALL)
• Create a configuration file named "config.ini" and enter the following (substituting the required information with your MySQL credentials):

[DATABASE]
HOST   = [MySQL Host]
PORT   = [MySQL Port]
USER   = [MySQL Username]
PASSWD = [MySQL Password]
DB     = fathmm

• Download "fathmm.py" from the ./cgi-bin folder and place it in the same directory as "config.ini"

Running our Software

In it's simplest form, our software parses dbSNP rs IDs and protein missense mutations from <INPUT> and returns a list of predictions weighted for inherited-disease mutations (Human) in <OUTPUT>. Furthermore, we return predictions on disease-associations when a mutation falls within a SUPERFAMILY domain.

python fathmm.py -i <INPUT> -o <OUTPUT>

A combination of the below is accepted/valid input:

• Human dbSNP rs IDs (dbSNP 137) - multiple SNPs should be entered on separate lines.
• Human SwissProt/TrEMBL and/or Ensembl protein identifiers followed by the amino acid substitution in the conventional one letter format - multiple substitutions can be entered on a single line and should be separated by a comma.

rs137854462
rs28936683
rs121908258
rs17132395
rs121912297
P43026 L441P
P35555 N548I,E1073K,C2307S 

Optional Parameters

The --help parameter can be used to view additional program parameters. In brief, there are two optional parameters:

• -w [?]

An optional parameter which controls the prediction algorithm used in our software:

Inherited  : return predictions weighted for human inherited-disease mutations [this is the default]
Unweighted : return unweighted (species-independant) predictions 
Cancer     : return predictions weighted specifically for Human cancer

• -p [?]

An optional parameter which controls the phenotype ontology used in our software:

DO : Disease Ontology [this is the default]
GO : Gene Ontology
HP : Human Phenotype Ontology
MP : Mouse Phenotype Ontology
WP : Worm Phenotype Ontology
YP : Yeast Phenotype Ontology
FP : Fly Phenotype Ontology
FA : Fly Anatomy Ontology
ZA : Zebrafish Anatomy Ontology
AP : Arabidopsis Plant Ontology
KW : UniProtKB KeyWords

Contributing:

We welcome any comments and/or suggestions that you may have regarding our software and server - please send an email directly to fathmm@biocompute.org.uk