diff --git a/debian/changelog b/debian/changelog index 274ab66..a5cdff3 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,4 +1,4 @@ -tigr-glimmer (3.02b-3) UNRELEASED; urgency=medium +tigr-glimmer (3.02b-3) unstable; urgency=medium [ Steffen Möller ] * Updated d/u/metadata @@ -15,8 +15,9 @@ * Trim trailing whitespace. * Wrap long lines in changelog entries: 2.13-1. * Refer to specific version of license GPL-2+. + * Do not use docbook-to-man to create manpages - -- Andreas Tille Wed, 29 Apr 2020 22:52:39 +0200 + -- Andreas Tille Wed, 29 Apr 2020 22:53:42 +0200 tigr-glimmer (3.02b-2) unstable; urgency=medium diff --git a/debian/control b/debian/control index a529c37..9635bb5 100644 --- a/debian/control +++ b/debian/control @@ -4,8 +4,7 @@ Andreas Tille Section: science Priority: optional -Build-Depends: debhelper-compat (= 12), - docbook-to-man +Build-Depends: debhelper-compat (= 12) Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/tigr-glimmer Vcs-Git: https://salsa.debian.org/med-team/tigr-glimmer.git diff --git a/debian/glimmer2_mans/tigr-anomaly.1 b/debian/glimmer2_mans/tigr-anomaly.1 new file mode 100644 index 0000000..ea79b47 --- /dev/null +++ b/debian/glimmer2_mans/tigr-anomaly.1 @@ -0,0 +1,32 @@ +.TH "TIGR-GLIMMER" "1" +.SH "NAME" +tigr-glimmer \(em The program lacks a description +.SH "SYNOPSIS" +.PP +\fBtigr-anomaly\fR [>dna-file] [>coord-file] +.SH "DESCRIPTION" +.PP +.SH "OPTIONS" +.SH "SEE ALSO" +.PP +tigr-glimmer3 (1), +tigr-adjust (1), +tigr-anomaly (1), +tigr-build-icm (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), +.PP +http://www.tigr.org/software/glimmer/ +.PP +Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3. +.SH "AUTHOR" +.PP +This manual page was quickly copied from the glimmer web site by Steffen Moeller moeller@debian.org for +the \fBDebian\fP system. + +.\" created by instant / docbook-to-man diff --git a/debian/glimmer2_mans/tigr-anomaly.sgml b/debian/glimmer2_mans/tigr-anomaly.sgml deleted file mode 100644 index 807de64..0000000 --- a/debian/glimmer2_mans/tigr-anomaly.sgml +++ /dev/null @@ -1,124 +0,0 @@ - manpage.1'. You may view - the manual page with: `docbook-to-man manpage.sgml | nroff -man | - less'. A typical entry in a Makefile or Makefile.am is: - -manpage.1: manpage.sgml - docbook-to-man $< > $@ - - - The docbook-to-man binary is found in the docbook-to-man package. - Please remember that if you create the nroff version in one of the - debian/rules file targets (such as build), you will need to include - docbook-to-man in your Build-Depends control field. - - --> - - - Steffen"> - Möller"> - - November 10, 2004"> - 1"> - moeller@debian.org"> - - TIGR-GLIMMER"> - - - Debian"> - GNU"> - GPL"> -]> - - - -
- &dhemail; -
- - &dhfirstname; - &dhsurname; - - - 2003 - &dhusername; - - &dhdate; - - - &dhucpackage; - - &dhsection; - - - &dhpackage; - - -The program lacks a description - - - - - tigr-anomaly - >dna-file - >coord-file - - - - DESCRIPTION - - - - - - OPTIONS - - - SEE ALSO - -tigr-glimmer3 (1), -tigr-adjust (1), -tigr-anomaly (1), -tigr-build-icm (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 by &dhusername; &dhemail; for - the &debian; system. - - - - - - diff --git a/debian/glimmer2_mans/tigr-build-icm.1 b/debian/glimmer2_mans/tigr-build-icm.1 new file mode 100644 index 0000000..943ade3 --- /dev/null +++ b/debian/glimmer2_mans/tigr-build-icm.1 @@ -0,0 +1,80 @@ +.TH "TIGR-GLIMMER \fB(1)\fP " "1" +.SH "NAME" +tigr-glimmer \(em Creates and outputs an interpolated Markov model(IMM) +.SH "SYNOPSIS" +.PP +\fBtigr-build-icm\fR +.SH "DESCRIPTION" +.PP +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. +.PP +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. +.PP +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: +.PP +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)) +.PP +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 +.PP +To run the program: +.PP +build-icm train.model +.PP +This will use the training data in train.seq to produce the file +train.model, containing your IMM. +.SH "SEE ALSO" +.PP +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), + +.PP +http://www.tigr.org/software/glimmer/ +.PP +Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3. +.SH "AUTHOR" +.PP +This manual page was quickly copied from the glimmer web site and readme file by Steffen Moeller moeller@debian.org for +the \fBDebian\fP system. + +.\" created by instant / docbook-to-man diff --git a/debian/glimmer2_mans/tigr-build-icm.sgml b/debian/glimmer2_mans/tigr-build-icm.sgml deleted file mode 100644 index 917339f..0000000 --- a/debian/glimmer2_mans/tigr-build-icm.sgml +++ /dev/null @@ -1,162 +0,0 @@ - manpage.1'. You may view - the manual page with: `docbook-to-man manpage.sgml | nroff -man | - less'. A typical entry in a Makefile or Makefile.am is: - -manpage.1: manpage.sgml - docbook-to-man $< > $@ - - - The docbook-to-man binary is found in the docbook-to-man package. - Please remember that if you create the nroff version in one of the - debian/rules file targets (such as build), you will need to include - docbook-to-man in your Build-Depends control field. - - --> - - - Steffen"> - Möller"> - - Novemver 10, 2004"> - 1"> - moeller@debian.org"> - - TIGR-GLIMMER"> - <!ENTITY dhpackage "tigr-glimmer"> - - <!ENTITY debian "<productname>Debian</productname>"> - <!ENTITY gnu "<acronym>GNU</acronym>"> - <!ENTITY gpl "&gnu; <acronym>GPL</acronym>"> -]> - -<refentry> - <refentryinfo> - <address> - &dhemail; - </address> - <author> - &dhfirstname; - &dhsurname; - </author> - <copyright> - <year>2003</year> - <holder>&dhusername;</holder> - </copyright> - &dhdate; - </refentryinfo> - <refmeta> - &dhucpackage; - - &dhsection; - </refmeta> - <refnamediv> - <refname>&dhpackage;</refname> - <refpurpose>Creates and outputs an interpolated Markov model(IMM)</refpurpose> - </refnamediv> - <refsynopsisdiv> - <cmdsynopsis> - <command>tigr-build-icm</command> - </cmdsynopsis> - </refsynopsisdiv> - <refsect1> - <title>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 &dhusername; &dhemail; for - the &debian; system. - - - - - - - - diff --git a/debian/glimmer2_mans/tigr-extract.1 b/debian/glimmer2_mans/tigr-extract.1 new file mode 100644 index 0000000..a93bbc9 --- /dev/null +++ b/debian/glimmer2_mans/tigr-extract.1 @@ -0,0 +1,67 @@ +.TH "TIGR-GLIMMER" "1" +.SH "NAME" +tigr-glimmer \(em Fine start/stop positions of genes in genome sequence +.SH "SYNOPSIS" +.PP +\fBtigr-extract\fR [genome-file \fB\fIoptions\fR\fP] +.SH "DESCRIPTION" +.PP +Program extract takes a FASTA format sequence file and a file +with a list of start/stop positions in that file (e.g., as produced +by the long-orfs program) and extracts and outputs the +specified sequences. +.PP +The first command-line argument is the name of the sequence file, +which must be in FASTA format. +.PP +The second command-line argument is the name of the coordinate file. +It must contain a list of pairs of positions in the first file, one +per line. The format of each entry is: +.PP +> +.PP +This file should contain no other information, so if you're using +the output of glimmer or long-orfs , you'll have to cut off +header lines. +.PP +The output of the program goes to the standard output and has one +line for each line in the coordinate file. Each line contains +the IDstring , followed by white space, followed by the substring +of the sequence file specified by the coordinate pair. Specifically, +the substring starts at the first position of the pair and ends at +the second position (inclusive). If the first position is bigger +than the second, then the DNA reverse complement of each position +is generated. Start/stop pairs that "wrap around" the end of the +genome are allowed. +.SH "OPTIONS" +.IP "\fB-skip\fP" 10 +makes the output omit the first 3 characters of each sequence, i.e., it skips over the start codon. This was the behaviour of the previous version of the program. +.IP "\fB-l\fP" 10 +makes the output omit an sequences shorter than n characters. +n includes the 3 skipped characters if the \-skip switch +is one. + +.SH "SEE ALSO" +.PP +tigr-glimmer3 (1), +tigr-long-orfs (1), +tigr-adjust (1), +tigr-anomaly (1), +tigr-build-icm (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), +.PP +http://www.tigr.org/software/glimmer/ +.PP +Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3. +.SH "AUTHOR" +.PP +This manual page was quickly copied from the glimmer web site by Steffen Moeller moeller@debian.org for +the \fBDebian\fP system. + +.\" created by instant / docbook-to-man diff --git a/debian/glimmer2_mans/tigr-extract.sgml b/debian/glimmer2_mans/tigr-extract.sgml deleted file mode 100644 index f701860..0000000 --- a/debian/glimmer2_mans/tigr-extract.sgml +++ /dev/null @@ -1,165 +0,0 @@ - manpage.1'. You may view - the manual page with: `docbook-to-man manpage.sgml | nroff -man | - less'. A typical entry in a Makefile or Makefile.am is: - -manpage.1: manpage.sgml - docbook-to-man $< > $@ - - - The docbook-to-man binary is found in the docbook-to-man package. - Please remember that if you create the nroff version in one of the - debian/rules file targets (such as build), you will need to include - docbook-to-man in your Build-Depends control field. - - --> - - - Steffen"> - Möller"> - - November 10, 2004"> - 1"> - moeller@debian.org"> - - TIGR-GLIMMER"> - - - Debian"> - GNU"> - GPL"> -]> - - - -
- &dhemail; -
- - &dhfirstname; - &dhsurname; - - - 2003 - &dhusername; - - &dhdate; - - - &dhucpackage; - - &dhsection; - - - &dhpackage; - - -Fine start/stop positions of genes in genome sequence - - - - - tigr-extract - genome-file - - - - DESCRIPTION - -Program extract takes a FASTA format sequence file and a file -with a list of start/stop positions in that file (e.g., as produced -by the long-orfs program) and extracts and outputs the -specified sequences. - -The first command-line argument is the name of the sequence file, -which must be in FASTA format. - -The second command-line argument is the name of the coordinate file. -It must contain a list of pairs of positions in the first file, one -per line. The format of each entry is: - <IDstring>> <start position> <stop position> -This file should contain no other information, so if you're using -the output of glimmer or long-orfs , you'll have to cut off -header lines. - -The output of the program goes to the standard output and has one -line for each line in the coordinate file. Each line contains -the IDstring , followed by white space, followed by the substring -of the sequence file specified by the coordinate pair. Specifically, -the substring starts at the first position of the pair and ends at -the second position (inclusive). If the first position is bigger -than the second, then the DNA reverse complement of each position -is generated. Start/stop pairs that "wrap around" the end of the -genome are allowed. - - - - OPTIONS - - - - - makes the output omit the first 3 characters of each sequence, i.e., it skips over the start codon. This was the behaviour of the previous version of the program. - - - - - makes the output omit an sequences shorter than n characters. - n includes the 3 skipped characters if the -skip switch - is one. - - - - - - SEE ALSO - -tigr-glimmer3 (1), -tigr-long-orfs (1), -tigr-adjust (1), -tigr-anomaly (1), -tigr-build-icm (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 by &dhusername; &dhemail; for - the &debian; system. - - - - - - - - diff --git a/debian/glimmer2_mans/tigr-glimmer.1 b/debian/glimmer2_mans/tigr-glimmer.1 new file mode 100644 index 0000000..c4528f9 --- /dev/null +++ b/debian/glimmer2_mans/tigr-glimmer.1 @@ -0,0 +1,39 @@ +.TH TIGR-GLIMMER 1 "April 16, 2008" +.SH NAME +tigr-glimmer \- runs various programs of the TIGR Glimmer suite +.SH SYNOPSIS +.B tigr-glimmer +.B program +[arguments] +.SH DESCRIPTION +This manual page documents briefly the +.B tigr-glimmer +wrapper to the TIGR Glimmer programs. +This manual page was written for the Debian GNU/Linux distribution +because upstream does not provide this wrapper and it was invented +for Debian to avoid conflicts with other packages that might cause +a name space pollution. +.PP +\fBtigr-glimmer\fP is just a wrapper that invokes the various programs in +the TIGR Glimmer software package. You can get more detailed documentation +in /usr/share/doc/tigr-glimmer. Please note that the documentation there +is a part of the former version Glimmer 2. The version Glimmer 3 has +some features that were described in the notes.pdf document inside +the documentation directory. +.PP +The following programs are included: anomaly, build-fixed, build-icm, +entropy-profile, entropy-score, extract, glimmer3, long-orfs, multi-extract, +score-fixed, start-codon-distrib, test, uncovered and window-acgt. +.SH OPTIONS +There are no options. +.SH EXAMPLES +.IP tigr-glimmer\ build-icm +.IP tigr-glimmer\ long-orfs +.SH SEE ALSO +For the pre previously packaged version Glimmer2 some text files from +the documentation were turned to man pages for the Debian GNU/Linux +distribution by Steffen Moeller +.br +.SH AUTHORS +This manual page was written by Andreas Tille , for +the Debian GNU/Linux system (but may be used by others). diff --git a/debian/glimmer2_mans/tigr-glimmer3.1 b/debian/glimmer2_mans/tigr-glimmer3.1 new file mode 100644 index 0000000..2a5b284 --- /dev/null +++ b/debian/glimmer2_mans/tigr-glimmer3.1 @@ -0,0 +1,101 @@ +.TH "TIGR-GLIMMER" "1" +.SH "NAME" +tigr-glimmer \(em Find/Score potential genes in genome-file using the probability model in icm-file +.SH "SYNOPSIS" +.PP +\fBtigr-glimmer3\fR [\fB\fIgenome-file\fR\fP] [\fB\fIicm-file\fR\fP] [\fB\fI[options]\fR\fP] +.SH "DESCRIPTION" +.PP +\fBtigr-glimmer\fR is a system for finding genes in microbial DNA, especially the genomes of bacteria and archaea. \fBtigr-glimmer\fR (Gene Locator and Interpolated Markov Modeler) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA. The IMM approach, described in our Nucleic Acids Research paper on \fBtigr-glimmer\fR 1.0 and in our subsequent paper on \fBtigr-glimmer\fR 2.0, uses a combination of Markov models from 1st through 8th-order, weighting each model according to its predictive power. \fBtigr-glimmer\fR 1.0 and 2.0 use 3-periodic nonhomogenous Markov models in their IMMs. +.PP +\fBtigr-glimmer\fR is the primary microbial gene finder at TIGR, and has been used to annotate the complete genomes of B. burgdorferi (Fraser et al., Nature, Dec. 1997), T. pallidum (Fraser et al., Science, July 1998), T. maritima, D. radiodurans, M. tuberculosis, and non-TIGR projects including C. trachomatis, C. pneumoniae, and others. Its analyses of some of these genomes and others is available at the TIGR microbial database site. +.PP +A special version of \fBtigr-glimmer\fR designed for small eukaryotes, GlimmerM, was used to find the genes in chromosome 2 of the malaria parasite, P. falciparum.. GlimmerM is described in S.L. Salzberg, M. Pertea, A.L. Delcher, M.J. Gardner, and H. Tettelin, "Interpolated Markov models for eukaryotic gene finding," Genomics 59 (1999), 24-31. Click here (http://www.tigr.org/software/glimmerm/) to visit the GlimmerM site, which includes information on how to download the GlimmerM system. +.PP +The \fBtigr-glimmer\fR system consists of two main programs. The first of these is the training program, build-imm. This program takes an input set of sequences and builds and outputs the IMM for them. These sequences can be complete genes or just partial orfs. For a new genome, this training data can consist of those genes with strong database hits as well as very long open reading frames that are statistically almost certain to be genes. The second program is glimmer, which uses this IMM to identify putative genes in an entire genome. \fBtigr-glimmer\fR automatically resolves conflicts between most overlapping genes by choosing one of them. It also identifies genes that are suspected to truly overlap, and flags these for closer inspection by the user. These ``suspect'' gene candidates have been a very small percentage of the total for all the genomes analyzed thus far. +\fBtigr-glimmer\fR is a program that... +.SH "OPTIONS" +.IP "\fB-C \fIn\fR\fP" 10 +Use n as GC percentage of independent model +.IP "" 10 +Note: n should be a percentage, e.g., \-C 45.2 +.IP "\-f" 10 +Use ribosome-binding energy to choose start codon +.IP "\fB+f\fP" 10 +Use first codon in orf as start codon +.IP "\fB-g \fIn\fR\fP" 10 +Set minimum gene length to n +.IP "\fB-i \fIfilename\fR\fP" 10 +Use \fB\fIfilename\fR\fP to select regions of bases that are off +limits, so that no bases within that area will be examined + +.IP "\fB-l\fP" 10 +Assume linear rather than circular genome, i.e., no wraparound +.IP "\fB-L \fIfilename\fR\fP" 10 +Use filename to specify a list of orfs that should +be scored separately, with no overlap rules + +.IP "\fB-M\fP" 10 +Input is a multifasta file of separate genes to be scored +separately, with no overlap rules + +.IP "\fB-o \fIn\fR\fP" 10 +Set minimum overlap length to n. Overlaps shorter than this +are ignored. + +.IP "\fB-p \fIn\fR\fP" 10 +Set minimum overlap percentage to n%. Overlaps shorter than this percentage of *both* strings are ignored. + +.IP "\fB-q \fIn\fR\fP" 10 +Set the maximum length orf that can be rejected because of +the independent probability score column to (n \- 1) + +.IP "\fB-r\fP" 10 +Don't use independent probability score column + +.IP "\fB+r\fP" 10 +Use independent probability score column + +.IP "\fB-r\fP" 10 +Don't use independent probability score column + +.IP "\fB-s \fIs\fR\fP" 10 +Use string s as the ribosome binding pattern to find start codons. +.IP "\fB+S\fP" 10 +Do use stricter independent intergenic model that doesn't +give probabilities to in-frame stop codons. (Option is obsolete +since this is now the only behaviour + +.IP "\fB-t \fIn\fR\fP" 10 +Set threshold score for calling as gene to n. If the in-frame +score >= n, then the region is given a number and considered +a potential gene. + +.IP "\fB-w \fIn\fR \fP" 10 +Use "weak" scores on tentative genes n or longer. Weak +scores ignore the independent probability score. + +.SH "SEE ALSO" +.PP +tigr-adjust (1), +tigr-anomaly (1), +tigr-build-icm (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), +tigr-glimmer3 (1), +tigr-long-orfs (1) +.PP +http://www.tigr.org/software/glimmer/ +.PP +Please see the readme in /usr/share/doc/glimmer for a description on how to use Glimmer. +.SH "AUTHOR" +.PP +This manual page was quickly copied from the glimmer web site by Steffen Moeller moeller@debian.org for +the \fBDebian\fP system. + +.\" created by instant / docbook-to-man diff --git a/debian/glimmer2_mans/tigr-glimmer3.sgml b/debian/glimmer2_mans/tigr-glimmer3.sgml deleted file mode 100644 index c552f16..0000000 --- a/debian/glimmer2_mans/tigr-glimmer3.sgml +++ /dev/null @@ -1,246 +0,0 @@ - manpage.1'. You may view - the manual page with: `docbook-to-man manpage.sgml | nroff -man | - less'. A typical entry in a Makefile or Makefile.am is: - -manpage.1: manpage.sgml - docbook-to-man $< > $@ - - - The docbook-to-man binary is found in the docbook-to-man package. - Please remember that if you create the nroff version in one of the - debian/rules file targets (such as build), you will need to include - docbook-to-man in your Build-Depends control field. - - --> - - - Steffen"> - Möller"> - - November 10, 2004"> - 1"> - moeller@debian.org"> - - TIGR-GLIMMER"> - - - Debian"> - GNU"> - GPL"> -]> - - - -
- &dhemail; -
- - &dhfirstname; - &dhsurname; - - - 2003 - &dhusername; - - &dhdate; - - - &dhucpackage; - - &dhsection; - - - &dhpackage; - -Find/Score potential genes in genome-file using the probability model in icm-file - - - - - tigr-glimmer3 - - - - - - - DESCRIPTION - -&dhpackage; is a system for finding genes in microbial DNA, especially the genomes of bacteria and archaea. &dhpackage; (Gene Locator and Interpolated Markov Modeler) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA. The IMM approach, described in our Nucleic Acids Research paper on &dhpackage; 1.0 and in our subsequent paper on &dhpackage; 2.0, uses a combination of Markov models from 1st through 8th-order, weighting each model according to its predictive power. &dhpackage; 1.0 and 2.0 use 3-periodic nonhomogenous Markov models in their IMMs. - -&dhpackage; is the primary microbial gene finder at TIGR, and has been used to annotate the complete genomes of B. burgdorferi (Fraser et al., Nature, Dec. 1997), T. pallidum (Fraser et al., Science, July 1998), T. maritima, D. radiodurans, M. tuberculosis, and non-TIGR projects including C. trachomatis, C. pneumoniae, and others. Its analyses of some of these genomes and others is available at the TIGR microbial database site. - -A special version of &dhpackage; designed for small eukaryotes, GlimmerM, was used to find the genes in chromosome 2 of the malaria parasite, P. falciparum.. GlimmerM is described in S.L. Salzberg, M. Pertea, A.L. Delcher, M.J. Gardner, and H. Tettelin, "Interpolated Markov models for eukaryotic gene finding," Genomics 59 (1999), 24-31. Click here (http://www.tigr.org/software/glimmerm/) to visit the GlimmerM site, which includes information on how to download the GlimmerM system. - -The &dhpackage; system consists of two main programs. The first of these is the training program, build-imm. This program takes an input set of sequences and builds and outputs the IMM for them. These sequences can be complete genes or just partial orfs. For a new genome, this training data can consist of those genes with strong database hits as well as very long open reading frames that are statistically almost certain to be genes. The second program is glimmer, which uses this IMM to identify putative genes in an entire genome. &dhpackage; automatically resolves conflicts between most overlapping genes by choosing one of them. It also identifies genes that are suspected to truly overlap, and flags these for closer inspection by the user. These ``suspect'' gene candidates have been a very small percentage of the total for all the genomes analyzed thus far. - &dhpackage; is a program that... - - - OPTIONS - - - - - Use n as GC percentage of independent model - Note: n should be a percentage, e.g., -C 45.2 - - - - -fUse ribosome-binding energy to choose start codon - - - Use first codon in orf as start codon - - - Set minimum gene length to n - - - - - Use - to select regions of bases that are off - limits, so that no bases within that area will be examined - - - - - - Assume linear rather than circular genome, i.e., no wraparound - - - - Use filename to specify a list of orfs that should - be scored separately, with no overlap rules - - - - - Input is a multifasta file of separate genes to be scored - separately, with no overlap rules - - - - - - - Set minimum overlap length to n. Overlaps shorter than this - are ignored. - - - - - - - Set minimum overlap percentage to n%. Overlaps shorter than this percentage of *both* strings are ignored. - - - - - - - Set the maximum length orf that can be rejected because of - the independent probability score column to (n - 1) - - - - - - - - Don't use independent probability score column - - - - - - -Use independent probability score column - - - - - - - - Don't use independent probability score column - - - Use string s as the ribosome binding pattern to find start codons. - - - - - - - Do use stricter independent intergenic model that doesn't - give probabilities to in-frame stop codons. (Option is obsolete - since this is now the only behaviour - - - - - - Set threshold score for calling as gene to n. If the in-frame - score >= n, then the region is given a number and considered - a potential gene. - - - - - - Use "weak" scores on tentative genes n or longer. Weak - scores ignore the independent probability score. - - - - - - SEE ALSO - -tigr-adjust (1), -tigr-anomaly (1), -tigr-build-icm (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), -tigr-glimmer3 (1), -tigr-long-orfs (1) - - -http://www.tigr.org/software/glimmer/ - - Please see the readme in /usr/share/doc/glimmer for a description on how to use Glimmer. - - - AUTHOR - This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for - the &debian; system. - - - - - - - diff --git a/debian/glimmer2_mans/tigr-long-orfs.1 b/debian/glimmer2_mans/tigr-long-orfs.1 new file mode 100644 index 0000000..0354743 --- /dev/null +++ b/debian/glimmer2_mans/tigr-long-orfs.1 @@ -0,0 +1,137 @@ +.TH "LONG-ORFS" "1" +.SH "NAME" +long-orfs \(em Find/Score potential genes in genome-file using +the probability model in icm-file +.SH "SYNOPSIS" +.PP +\fBtigr-long-orgs\fR [genome-file \fB\fIoptions\fR\fP] +.SH "DESCRIPTION" +.PP +Program long-orfs takes a sequence file (in FASTA format) and +outputs a list of all long "potential genes" in it that do not +overlap by too much. By "potential gene" I mean the portion of +an orf from the first start codon to the stop codon at the end. +.PP +The first few lines of output specify the settings of various +parameters in the program: +.PP +Minimum gene length is the length of the smallest fragment +considered to be a gene. The length is measured from the first base +of the start codon to the last base *before* the stop codon. +This value can be specified when running the program with the \-g option. +By default, the program now (April 2003) will compute an optimal length +for this parameter, where "optimal" is the value that produces the +greatest number of long ORFs, thereby increasing the amount of data +used for training. +.PP +Minimum overlap length is a lower bound on the number of bases overlap +between 2 genes that is considered a problem. Overlaps shorter than +this are ignored. +.PP +Minimum overlap percent is another lower bound on the number of bases +overlap that is considered a problem. Overlaps shorter than this +percentage of *both* genes are ignored. +.PP +The next portion of the output is a list of potential genes: +.PP +Column 1 is an ID number for reference purposes. It is assigned +sequentially starting with 1 to all long potential genes. If +overlapping genes are eliminated, gaps in the numbers will occur. +The ID prefix is specified in the constant ID_PREFIX . +.PP +Column 2 is the position of the first base of the first start codon in +the orf. Currently I use atg, and gtg as start codons. This is +easily changed in the function Is_Start () . +.PP +Column 3 is the position of the last base *before* the stop codon. Stop +codons are taa, tag, and tga. Note that for orfs in the reverse +reading frames have their start position higher than the end position. +The order in which orfs are listed is in increasing order by +Max {OrfStart, End}, i.e., the highest numbered position in the orf, +except for orfs that "wrap around" the end of the sequence. +.PP +When two genes with ID numbers overlap by at least a sufficient +amount (as determined by Min_Olap and Min_Olap_Percent ), they +are eliminated and do not appear in the output. +.PP +The final output of the program (sent to the standard error file so +it does not show up when output is redirected to a file) is the +length of the longest orf found. +.PP + +Specifying Different Start and Stop Codons: +.PP +To specify different sets of start and stop codons, modify the file +gene.h . Specifically, the functions: +.PP +Is_Forward_Start Is_Reverse_Start Is_Start +Is_Forward_Stop Is_Reverse_Stop Is_Stop +.PP +are used to determine what is used for start and stop codons. +.PP +Is_Start and Is_Stop do simple string comparisons to specify +which patterns are used. To add a new pattern, just add the comparison +for it. To remove a pattern, comment out or delete the comparison +for it. +.PP +The other four functions use a bit comparison to determine start and +stop patterns. They represent a codon as a 12-bit pattern, with 4 bits +for each base, one bit for each possible value of the bases, T, G, C +or A. Thus the bit pattern 0010 0101 1100 represents the base +pattern [C] [A or G] [G or T]. By doing bit operations (& | ~) and +comparisons, more complicated patterns involving ambiguous reads +can be tested efficiently. Simple patterns can be tested as in +the current code. +.PP +For example, to insert an additional start codon of CAT requires 3 changes: +1. The line +|| (Codon & 0x218) == Codon +should be inserted into Is_Forward_Start , since 0x218 = 0010 0001 1000 +represents CAT. +2. The line +|| (Codon & 0x184) == Codon +should be inserted into Is_Reverse_Start , since 0x184 = 0001 1000 0100 +represents ATG, which is the reverse-complement of CAT. Alternately, +the #define constant ATG_MASK could be used. +3. The line +|| strncmp (S, "cat", 3) == 0 +should be inserted into Is_Start . +.SH "OPTIONS" +.IP "\fB-g \fIn\fR\fP" 10 +Set minimum gene length to n. Default is to compute an +optimal value automatically. Don't change this unless you +know what you're doing. +.IP "\fB-l\fP" 10 +Regard the genome as linear (not circular), i.e., do not allow +genes to "wrap around" the end of the genome. +This option works on both glimmer and long-orfs . +The default behavior is to regard the genome as circular. +.IP "\fB-o \fIn\fR\fP" 10 +Set maximum overlap length to n. Overlaps shorter than this +are permitted. (Default is 0 bp.) +.IP "\fB-p \fIn\fR\fP" 10 +Set maximum overlap percentage to n%. Overlaps shorter than +this percentage of *both* strings are ignored. (Default is 10%.) +.SH "SEE ALSO" +.PP +tigr-glimmer3 (1), +tigr-adjust (1), +tigr-anomaly (1), +tigr-build-icm (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), +.PP +http://www.tigr.org/software/glimmer/ +.PP +Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3. +.SH "AUTHOR" +.PP +This manual page was quickly copied from the glimmer web site by Steffen Moeller moeller@debian.org for +the \fBDebian\fP system. + +.\" created by instant / docbook-to-man diff --git a/debian/glimmer2_mans/tigr-long-orfs.sgml b/debian/glimmer2_mans/tigr-long-orfs.sgml deleted file mode 100644 index a3922d1..0000000 --- a/debian/glimmer2_mans/tigr-long-orfs.sgml +++ /dev/null @@ -1,238 +0,0 @@ - manpage.1'. You may view - the manual page with: `docbook-to-man manpage.sgml | nroff -man | - less'. A typical entry in a Makefile or Makefile.am is: - -manpage.1: manpage.sgml - docbook-to-man $< > $@ - - - The docbook-to-man binary is found in the docbook-to-man package. - Please remember that if you create the nroff version in one of the - debian/rules file targets (such as build), you will need to include - docbook-to-man in your Build-Depends control field. - - --> - - - Steffen"> - Möller"> - - November 10, 2004"> - 1"> - moeller@debian.org"> - - LONG-ORFS"> - - - Debian"> - GNU"> - GPL"> -]> - - - -
- &dhemail; -
- - &dhfirstname; - &dhsurname; - - - 2003 - &dhusername; - - &dhdate; - - - &dhucpackage; - - &dhsection; - - - &dhpackage; - - -Find/Score potential genes in genome-file using -the probability model in icm-file - - - - - tigr-long-orgs - genome-file - - - - DESCRIPTION - -Program long-orfs takes a sequence file (in FASTA format) and -outputs a list of all long "potential genes" in it that do not -overlap by too much. By "potential gene" I mean the portion of -an orf from the first start codon to the stop codon at the end. - -The first few lines of output specify the settings of various -parameters in the program: - - Minimum gene length is the length of the smallest fragment - considered to be a gene. The length is measured from the first base - of the start codon to the last base *before* the stop codon. - This value can be specified when running the program with the -g option. - By default, the program now (April 2003) will compute an optimal length - for this parameter, where "optimal" is the value that produces the - greatest number of long ORFs, thereby increasing the amount of data - used for training. - - Minimum overlap length is a lower bound on the number of bases overlap - between 2 genes that is considered a problem. Overlaps shorter than - this are ignored. - - Minimum overlap percent is another lower bound on the number of bases - overlap that is considered a problem. Overlaps shorter than this - percentage of *both* genes are ignored. - -The next portion of the output is a list of potential genes: - - Column 1 is an ID number for reference purposes. It is assigned - sequentially starting with 1 to all long potential genes. If - overlapping genes are eliminated, gaps in the numbers will occur. - The ID prefix is specified in the constant ID_PREFIX . - - Column 2 is the position of the first base of the first start codon in - the orf. Currently I use atg, and gtg as start codons. This is - easily changed in the function Is_Start () . - - Column 3 is the position of the last base *before* the stop codon. Stop - codons are taa, tag, and tga. Note that for orfs in the reverse - reading frames have their start position higher than the end position. - The order in which orfs are listed is in increasing order by - Max {OrfStart, End}, i.e., the highest numbered position in the orf, - except for orfs that "wrap around" the end of the sequence. - -When two genes with ID numbers overlap by at least a sufficient -amount (as determined by Min_Olap and Min_Olap_Percent ), they -are eliminated and do not appear in the output. - -The final output of the program (sent to the standard error file so -it does not show up when output is redirected to a file) is the -length of the longest orf found. - - - -Specifying Different Start and Stop Codons: - -To specify different sets of start and stop codons, modify the file -gene.h . Specifically, the functions: - - Is_Forward_Start Is_Reverse_Start Is_Start - Is_Forward_Stop Is_Reverse_Stop Is_Stop - -are used to determine what is used for start and stop codons. - -Is_Start and Is_Stop do simple string comparisons to specify -which patterns are used. To add a new pattern, just add the comparison -for it. To remove a pattern, comment out or delete the comparison -for it. - -The other four functions use a bit comparison to determine start and -stop patterns. They represent a codon as a 12-bit pattern, with 4 bits -for each base, one bit for each possible value of the bases, T, G, C -or A. Thus the bit pattern 0010 0101 1100 represents the base -pattern [C] [A or G] [G or T]. By doing bit operations (& | ~) and -comparisons, more complicated patterns involving ambiguous reads -can be tested efficiently. Simple patterns can be tested as in -the current code. - -For example, to insert an additional start codon of CAT requires 3 changes: -1. The line - || (Codon & 0x218) == Codon - should be inserted into Is_Forward_Start , since 0x218 = 0010 0001 1000 - represents CAT. -2. The line - || (Codon & 0x184) == Codon - should be inserted into Is_Reverse_Start , since 0x184 = 0001 1000 0100 - represents ATG, which is the reverse-complement of CAT. Alternately, - the #define constant ATG_MASK could be used. -3. The line - || strncmp (S, "cat", 3) == 0 - should be inserted into Is_Start . - - - - - OPTIONS - - - - - Set minimum gene length to n. Default is to compute an - optimal value automatically. Don't change this unless you - know what you're doing. - - - - Regard the genome as linear (not circular), i.e., do not allow - genes to "wrap around" the end of the genome. - This option works on both glimmer and long-orfs . - The default behavior is to regard the genome as circular. - - - Set maximum overlap length to n. Overlaps shorter than this - are permitted. (Default is 0 bp.) - - - Set maximum overlap percentage to n%. Overlaps shorter than - this percentage of *both* strings are ignored. (Default is 10%.) - - - - - SEE ALSO - -tigr-glimmer3 (1), -tigr-adjust (1), -tigr-anomaly (1), -tigr-build-icm (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 by &dhusername; &dhemail; for - the &debian; system. - - - - - - diff --git a/debian/glimmer2_mans/tigr-run-glimmer3.1 b/debian/glimmer2_mans/tigr-run-glimmer3.1 new file mode 100644 index 0000000..6fe2309 --- /dev/null +++ b/debian/glimmer2_mans/tigr-run-glimmer3.1 @@ -0,0 +1,33 @@ +.TH "TIGR-GLIMMER" "1" +.SH "NAME" +tigr-glimmer \(em Apply the suite of programs within glimmer3 to a a prokaryotic or archean genome. +.SH "SYNOPSIS" +.PP +\fBtigr-run-glimmer3\fR +.SH "DESCRIPTION" +.PP +A shell script that wraps a set of tigr-* utilities of the glimmer package to retrieve coding regions. +.SH "SEE ALSO" +.PP +tigr-glimmer3 (1), +tigr-adjust (1), +tigr-anomaly (1), +tigr-build-icm (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), +tigr-long-orfs (1), +.PP +http://www.tigr.org/software/glimmer/ +.PP +Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3. +.SH "AUTHOR" +.PP +This manual page was quickly copied from the glimmer web site by Steffen Moeller moeller@debian.org for +the \fBDebian\fP system. + +.\" created by instant / docbook-to-man diff --git a/debian/glimmer2_mans/tigr-run-glimmer3.sgml b/debian/glimmer2_mans/tigr-run-glimmer3.sgml deleted file mode 100644 index abee996..0000000 --- a/debian/glimmer2_mans/tigr-run-glimmer3.sgml +++ /dev/null @@ -1,120 +0,0 @@ - manpage.1'. You may view - the manual page with: `docbook-to-man manpage.sgml | nroff -man | - less'. A typical entry in a Makefile or Makefile.am is: - -manpage.1: manpage.sgml - docbook-to-man $< > $@ - - - The docbook-to-man binary is found in the docbook-to-man package. - Please remember that if you create the nroff version in one of the - debian/rules file targets (such as build), you will need to include - docbook-to-man in your Build-Depends control field. - - --> - - - Steffen"> - Möller"> - - November 10, 2004"> - 1"> - moeller@debian.org"> - - TIGR-GLIMMER"> - - - Debian"> - GNU"> - GPL"> -]> - - - -
- &dhemail; -
- - &dhfirstname; - &dhsurname; - - - 2003 - &dhusername; - - &dhdate; - - - &dhucpackage; - - &dhsection; - - - &dhpackage; - - -Apply the suite of programs within glimmer3 to a a prokaryotic or archean genome. - - - - - tigr-run-glimmer3 - - - - DESCRIPTION - -A shell script that wraps a set of tigr-* utilities of the glimmer package to retrieve coding regions. - - - - SEE ALSO - -tigr-glimmer3 (1), -tigr-adjust (1), -tigr-anomaly (1), -tigr-build-icm (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), -tigr-long-orfs (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 by &dhusername; &dhemail; for - the &debian; system. - - - - - - diff --git a/debian/manpages b/debian/manpages index 5ff77c4..7b4c52f 100644 --- a/debian/manpages +++ b/debian/manpages @@ -1,2 +1 @@ -debian/*.1 debian/glimmer2_mans/*.1 diff --git a/debian/rules b/debian/rules index 67cda3e..ade7f12 100755 --- a/debian/rules +++ b/debian/rules @@ -1,18 +1,6 @@ #!/usr/bin/make -f export DEB_BUILD_MAINT_OPTIONS = hardening=+all - -MANPAGES=debian/glimmer2_mans/tigr-anomaly.1 \ - debian/glimmer2_mans/tigr-build-icm.1 \ - debian/glimmer2_mans/tigr-extract.1 \ - debian/glimmer2_mans/tigr-glimmer3.1 \ - debian/glimmer2_mans/tigr-long-orfs.1 \ - debian/glimmer2_mans/tigr-run-glimmer3.1 - -.SUFFIXES: .1 .sgml - -.sgml.1: - docbook-to-man $< > $@ %: dh $@ diff --git a/debian/tigr-glimmer.1 b/debian/tigr-glimmer.1 deleted file mode 100644 index c4528f9..0000000 --- a/debian/tigr-glimmer.1 +++ /dev/null @@ -1,39 +0,0 @@ -.TH TIGR-GLIMMER 1 "April 16, 2008" -.SH NAME -tigr-glimmer \- runs various programs of the TIGR Glimmer suite -.SH SYNOPSIS -.B tigr-glimmer -.B program -[arguments] -.SH DESCRIPTION -This manual page documents briefly the -.B tigr-glimmer -wrapper to the TIGR Glimmer programs. -This manual page was written for the Debian GNU/Linux distribution -because upstream does not provide this wrapper and it was invented -for Debian to avoid conflicts with other packages that might cause -a name space pollution. -.PP -\fBtigr-glimmer\fP is just a wrapper that invokes the various programs in -the TIGR Glimmer software package. You can get more detailed documentation -in /usr/share/doc/tigr-glimmer. Please note that the documentation there -is a part of the former version Glimmer 2. The version Glimmer 3 has -some features that were described in the notes.pdf document inside -the documentation directory. -.PP -The following programs are included: anomaly, build-fixed, build-icm, -entropy-profile, entropy-score, extract, glimmer3, long-orfs, multi-extract, -score-fixed, start-codon-distrib, test, uncovered and window-acgt. -.SH OPTIONS -There are no options. -.SH EXAMPLES -.IP tigr-glimmer\ build-icm -.IP tigr-glimmer\ long-orfs -.SH SEE ALSO -For the pre previously packaged version Glimmer2 some text files from -the documentation were turned to man pages for the Debian GNU/Linux -distribution by Steffen Moeller -.br -.SH AUTHORS -This manual page was written by Andreas Tille , for -the Debian GNU/Linux system (but may be used by others).