CD-HIT

Introduction

CD-HIT was originally a protein clustering program. The main advantage of this program is its ultra-fast speed. It can be hundreds of times than other clustering programs, for example BLASTCLUST. Therefore it can handle very large databases, like NR. The first version was released in 2001, the second version was publishes in 2002 with significant improvements. Since 2004 its hosted at bioinformatics.org as an open source project which helped to develop the program even more. Its still under active development and there will be new features and programs out in the future.

Installed Version

The currently installed version is 4.6.4.

Using BLAT with the HPC Cluster

If you want to find out more about BLAT on the HPC Cluster, you can use the command

module spider blat

This will show you basic informations e.g. a short description and the currently installed version.

To load the desired version of the module, use the command, e.g.

module load BLAT

Always remember: this command is case sensitive!

After loading the module, you can run BLAT by using following command

blat <database> <query> [-ooc=11.ooc] output.psl

By adding the -occ flag you will most likely speed up your search, although you might not find certain sequences. If you can afford extra processing time, you may want to run blat without the -ooc=11.ooc flag if your particular situation warrants its use.

Documentation

The full documentation can be found here.