Free Knowledge Resources


Linux Manual Pages


Free Software * Books

Source Code

Free Media

Linux

tigr-build-icm(1)


NAME

   tigr-glimmer --- Creates 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  reference
   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
   combination 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
   SAMPLE_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)



Opportunity


Personal Opportunity - Free software gives you access to billions of dollars of software at no cost. Use this software for your business, personal use or to develop a profitable skill. Access to source code provides access to a level of capabilities/information that companies protect though copyrights. Open source is a core component of the Internet and it is available to you. Leverage the billions of dollars in resources and capabilities to build a career, establish a business or change the world. The potential is endless for those who understand the opportunity.

Business Opportunity - Goldman Sachs, IBM and countless large corporations are leveraging open source to reduce costs, develop products and increase their bottom lines. Learn what these companies know about open source and how open source can give you the advantage.



Free Software


Free Software provides computer programs and capabilities at no cost but more importantly, it provides the freedom to run, edit, contribute to, and share the software. The importance of free software is a matter of access, not price. Software at no cost is a benefit but ownership rights to the software and source code is far more significant.

Free Office Software - The Libre Office suite provides top desktop productivity tools for free. This includes, a word processor, spreadsheet, presentation engine, drawing and flowcharting, database and math applications. Libre Office is available for Linux or Windows.



Free Books


The Free Books Library is a collection of thousands of the most popular public domain books in an online readable format. The collection includes great classical literature and more recent works where the U.S. copyright has expired. These books are yours to read and use without restrictions.

Source Code - Want to change a program or know how it works? Open Source provides the source code for its programs so that anyone can use, modify or learn how to write those programs themselves. Visit the GNU source code repositories to download the source.



Education


Study at Harvard, Stanford or MIT - Open edX provides free online courses from Harvard, MIT, Columbia, UC Berkeley and other top Universities. Hundreds of courses for almost all major subjects and course levels. Open edx also offers some paid courses and selected certifications.

Linux Manual Pages - A man or manual page is a form of software documentation found on Linux/Unix operating systems. Topics covered include computer programs (including library and system calls), formal standards and conventions, and even abstract concepts.


birds banner