PHAT

PHAT is a Pretty Handy Annotation Tool for finding genes in eukaryotic organisms. It was originally developed with a view to annotating Plasmodium falciparum but now comes with code to retrain it for other organisms. (Requires annotated GenBank files for input.)

The latest version comes with ready-made parameter sets for the analysis of:

• Homo sapiens
• Plasmodium falciparum
• Plasmodium vivax

Phat supports most input sequence formats and has support for analyzing sequences in parallel on multiple-processor machines.

Installed on the opteron cluster.

Usage

Phat takes its parameters from several files all located in the same directory.

At PSC, that directory is /home/biomed/src/Phat/Phat/Pars.

There are two ways to tell the program which set of parameters to use. One is to specify the directory on the command line:

fullphat -p /home/biomed/src/Phat/Phat/Pars myseq.fasta
halfphat -p /home/biomed/src/Phat/Phat/Pars myseq.gbk

Another way is to set the environment variable PHATPARS:

setenv PHATPARS /home/biomed/src/Phat/Phat/Pars
fullphat myseq.fasta

The -p option will override the environment variable if it is already set.

Input sequences can be in fasta or genbank format. If a multiple fasta file is passed in only the first sequence in the file will be analyzed.

Other documentation

• The PHAT README file, which contains detailed descriptions of usage.
• The PHAT website

See also:

• Other sequence analysis software installed at PSC.