This software was last updated 9/17/2014. Questions, comments, suggestions, etc?
Send emails to nick.zhangyuan@gmail.com
- Clone the repository:
git clone git@github.com:zhangy72/PseudoDomain.git
-
g++ compiler is required in your Unix/Linux system. To install component bin files of PseudoDomain, run the Makeme file using the following command:
make -
Make sure all .sh files and hmmframe are executable in your environment. If not, you can use the command:
chmod 755 *.sh
chmod 755 hmmframe
- Python is required in your Unix/Linux system and in the path.
To run PseudoDomain pipeline, enter the folder of PseudoDomain and use the following command:
./PseudoDomain.sh -m <Pfam HMM file> -f <fasta file> -o <output file> [other options]
Options:
-h: show this message
-c: domain coverage threshold (default: 0.5)
The hmm file should be in HMMER3.0's hmm file format. It is recommended you download the Pfam-A.hmm file from Pfam (http://pfam.xfam.org/). The nucleotide sequence file should be in fasta format.
The output file specifies the following fields of the identified processed pseudogene:
[input sequence name] [protein domains separated by comma] [beginning position] [ending position] [stop codon number] [frameshift number]
PseudoDomain can be referenced as:
Copyright (C) 2014, Yuan Zhang and Yanni Sun.
You may redistribute this software under the terms of GNU GENERAL PUBLIC LICENSE.