Copyright (C) Juan Miguel Cejuela <juanmi@jmcejuela.com>

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clTMHMM: TMHMM-based TM Protein Topology Predictor in CL
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Compatibility: ANSI Common Lisp. Any SO
Dependencies: jmc.cl.utils, cl-hmm
Originally Created:    Wed Jul  9 18:18:18 2008 (CEST)
Last Effective Update: Mon Sep 22 11:11:22 2008 (CEST)




Description:
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Simple Transmembrane Protein Topology Predictor modeled with
a Hidden Markov Model and written in Common Lisp.

Constructed after the TMHMM 1.0 architecture by Krogh et
al. in 2001 which was a huge advance in the time it
appeared. In the last couple of years others predictors have
been created or improved, with special attention to TMHMM 2.0
(and the newest Phobius), PRODIV-HMM, HMMTOP 2.0, or
PHDhtm. Results yielded with this predictor are comparable
to the former model.

Program created to show the capabilities of the CL-HMM
library in a work of computer science rather than
bioinformatics. Several improvements could be achieved taking
into account last insights in the field.



Features:
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 - Use of a HMM following the TMHMM 1.0 model.
 - No signal peptides are modeled nor treated.


Files Definition:
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	cltmhmm.asd: System definer

	packages: package definer

	cltmhmm: model and base

	predictor: functions to predict a topology

	accuracy-validation: given the real topology, check the
			     accuracy of the predicted one

	other-results-interpreter: interpreter for other predictors:
				   -TMHMM 1.0, 2.0, Phobius, and
				   derived