tigr-build-icm(1) [debian man page]

TIGR-GLIMMER	 (1)   (1)				      General Commands Manual					TIGR-GLIMMER	 (1)   (1)

NAME

       tigr-glimmer -- Ceates and outputs an interpolated Markov model(IMM)

SYNOPSIS

       tigr-build-icm

DESCRIPTION

       Program	 build-icm.c   creates and outputs an interpolated Markov model (IMM) as described in the paper A.L. Delcher, D. Harmon, S. Kasif,
       O. White, and S.L. Salzberg.  Improved Microbial Gene Identification with Glimmer.  Nucleic Acids Research, 1999, in press.  Please  refer-
       ence this paper if you use the system as part of any published research.

       Input  comes  from the file named on the command-line.  Format should be one string per line.  Each line has an ID string followed by white
       space followed by the sequence itself.  The script run-glimmer3 generates an input file in the correct format using the 'extract' program.

       The IMM is constructed as follows: For a given context, say acgtta, we want to estimate the probability distribution of the next character.
       We  shall  do this as a linear combination of the observed probability distributions for this context and all of its suffixes, i.e., cgtta,
       gtta, tta, ta, a and empty.  By observed distributions I mean the counts of the number of occurrences of these strings in the training set.
       The  linear combination is determined by a set of probabilities, lambda, one for each context string.  For context acgtta the linear combi-
       nation coefficients are:

       lambda (acgtta) (1 - lambda (acgtta)) x lambda (cgtta) (1 - lambda (acgtta)) x (1 - lambda (cgtta)) x lambda (gtta) (1 - lambda (acgtta)) x
       (1  - lambda (cgtta)) x (1 - lambda (gtta)) x lambda (tta) (1 - lambda (acgtta)) x (1 - lambda (cgtta)) x (1 - lambda (gtta)) x (1 - lambda
       (tta))  x (1 - lambda (ta))  x (1 - lambda (a))

       We compute the lambda values for each context as follows: - If the number of observations in the training  set  is  >=  the  constant  SAM-
       PLE_SIZE_BOUND,	the  lambda for that context is 1.0 - Otherwise, do a chi-square test on the observations for this context compared to the
       distribution predicted for the one-character shorter suffix context.  If the chi-square significance < 0.5, set the lambda for this context
       to 0.0 Otherwise set the lambda for this context to: (chi-square significance) x (# observations) / SAMPLE_WEIGHT

       To run the program:

       build-icm <train.seq > train.model

       This will use the training data in train.seq to produce the file train.model, containing your IMM.

SEE ALSO

       tigr-glimmer3  (1),  tigr-long-orfs (1), tigr-adjust (1), tigr-anomaly	(1), tigr-extract (1), tigr-check (1), tigr-codon-usage (1), tigr-
       compare-lists (1), tigr-extract (1), tigr-generate (1), tigr-get-len (1), tigr-get-putative (1),

       http://www.tigr.org/software/glimmer/

       Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.

AUTHOR

       This manual page was quickly copied from the glimmer web site and readme file by Steffen Moeller moeller@debian.org for the Debian system.

															TIGR-GLIMMER	 (1)   (1)

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LEGENDRE(3)						User Contributed Perl Documentation					       LEGENDRE(3)

NAME

       PDL::GSLSF::LEGENDRE - PDL interface to GSL Special Functions

DESCRIPTION

       This is an interface to the Special Function package present in the GNU Scientific Library.

SYNOPSIS

Functions
FUNCTIONS

       gsl_sf_legendre_Pl

	 Signature: (double x(); double [o]y(); double [o]e(); int l)

       P_l(x)

       gsl_sf_legendre_Pl_array

	 Signature: (double x(); double [o]y(num); int l=>num)

       P_l(x) from 0 to n-1.

       gsl_sf_legendre_Ql

	 Signature: (double x(); double [o]y(); double [o]e(); int l)

       Q_l(x)

       gsl_sf_legendre_Plm

	 Signature: (double x(); double [o]y(); double [o]e(); int l; int m)

       P_lm(x)

       gsl_sf_legendre_Plm_array

	 Signature: (double x(); double [o]y(num); int l=>num; int m)

       P_lm(x) for l from 0 to n-2+m.

       gsl_sf_legendre_sphPlm

	 Signature: (double x(); double [o]y(); double [o]e(); int l; int m)

       P_lm(x), normalized properly for use in spherical harmonics

       gsl_sf_legendre_sphPlm_array

	 Signature: (double x(); double [o]y(num); int n=>num; int m)

       P_lm(x), normalized properly for use in spherical harmonics for l from 0 to n-2+m.

       gsl_sf_conicalP_half

	 Signature: (double x(); double [o]y(); double [o]e(); double lambda)

       Irregular Spherical Conical Function P^{1/2}_{-1/2 + I lambda}(x)

       gsl_sf_conicalP_mhalf

	 Signature: (double x(); double [o]y(); double [o]e(); double lambda)

       Regular Spherical Conical Function P^{-1/2}_{-1/2 + I lambda}(x)

       gsl_sf_conicalP_0

	 Signature: (double x(); double [o]y(); double [o]e(); double lambda)

       Conical Function P^{0}_{-1/2 + I lambda}(x)

       gsl_sf_conicalP_1

	 Signature: (double x(); double [o]y(); double [o]e(); double lambda)

       Conical Function P^{1}_{-1/2 + I lambda}(x)

       gsl_sf_conicalP_sph_reg

	 Signature: (double x(); double [o]y(); double [o]e(); int l; double lambda)

       Regular Spherical Conical Function P^{-1/2-l}_{-1/2 + I lambda}(x)

       gsl_sf_conicalP_cyl_reg_e

	 Signature: (double x(); double [o]y(); double [o]e(); int m; double lambda)

       Regular Cylindrical Conical Function P^{-m}_{-1/2 + I lambda}(x)

       gsl_sf_legendre_H3d

	 Signature: (double [o]y(); double [o]e(); int l; double lambda; double eta)

       lth radial eigenfunction of the Laplacian on the 3-dimensional hyperbolic space.

       gsl_sf_legendre_H3d_array

	 Signature: (double [o]y(num); int l=>num; double lambda; double eta)

       Array of H3d(ell), for l from 0 to n-1.

AUTHOR

       This file copyright (C) 1999 Christian Pellegrin <chri@infis.univ.trieste.it> All rights reserved. There is no warranty. You are allowed to
       redistribute this software / documentation under certain conditions. For details, see the file COPYING in the PDL distribution. If this
       file is separated from the PDL distribution, the copyright notice should be included in the file.

       The GSL SF modules were written by G. Jungman.

perl v5.8.0							    2003-01-29							       LEGENDRE(3)

Linux and UNIX Man Pages

tigr-build-icm(1) [debian man page]

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