fathmm

KO | EN

gitlite — search

#javascript #react #golang #android #machine-learning #rust #docker #nodejs #java #windows #awesome #kubernetes #vue #awesome-list

(★ 14)

The Functional Analysis through Hidden Markov Models Software and Server

fathmm 최신버젼 다운로드

최종 버전 다운로드 (.zip)

// repository documentation

Was this content helpful?

★ 0 (0 ratings)

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

fathmm

fathmm 최신버젼 다운로드

오늘의 추천 프로젝트

Was this content helpful?

Recent Feedback

fathmm

fathmm 최신버젼 다운로드

오늘의 추천 프로젝트

Was this content helpful?

Recent Feedback

Download README