clTMHMM

TMHMM-based TM Protein Topology Predictor in ANSI Common Lisp. Constructed after the TMHMM 1.0 architecture by Krogh et al. in 2001, obtaining a comparable accuracy. Newer and better predictors are TMHMM 2.0, Phobius, PRODIV-TMHMM, HMMTOP 2.0, or PHDhtm.

clTMHMM is implemented to demonstrate the capacities of CL-HMM. Several improvements could be achieved taking into account last insights in the topic.

Features

Use of a HMM following the TMHMM 1.0 model. Comparable accuracy
No signal peptides are modeled nor treated.
Off-line predictor, no graphical interface for the moment

Download

The latest stable version is the v0.2

Installation

Dependencies

CL-HMM depends on the following systems. Download them, and load them with asdf.

Actual Installation

Download the latest stable version of clTMHMM and load it with asdf, (asdf:operate 'asdf:load-op :cltmhmm)

Tutorial

To predict a given TM protein use predict-tmpt:


(predict-tmpt "MRRQKGMTLVEVLVALSVFALAGIAVLQTTARQASSLSRLEEKTFAGWVAENQQVQLRLEQRWPEASWVRGETQFAGLRWHWRWQGVETGDPQTKALDVEVRRNKDAFAADASLRTYVVKQ")
"# Identifier: 
# Description: 
# Length: 121
# Number of predicted TMHs: 1
    inside        1     11
    TMhelix       12    30
    output        31    121


"
"iiiiiiiiiiiMMMMMMMMMMMMMMMMMMMooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo"

Author

clTMHMM is written and maintained by Juan Miguel Cejuela (jmcejuela .a.t. gmail . com)