diff --git a/debian/long-orfs.1 b/debian/long-orfs.1 deleted file mode 100644 index bc57925..0000000 --- a/debian/long-orfs.1 +++ /dev/null @@ -1,190 +0,0 @@ -...\" $Header: /aolnet/dev/src/CVS/sgml/docbook-to-man/cmd/docbook-to-man.sh,v 1.1.1.1 1998/11/13 21:31:59 db3l Exp $ -...\" -...\" transcript compatibility for postscript use. -...\" -...\" synopsis: .P! -...\" -.de P! -.fl -\!!1 setgray -.fl -\\&.\" -.fl -\!!0 setgray -.fl \" force out current output buffer -\!!save /psv exch def currentpoint translate 0 0 moveto -\!!/showpage{}def -.fl \" prolog -.sy sed -e 's/^/!/' \\$1\" bring in postscript file -\!!psv restore -. -.de pF -.ie \\*(f1 .ds f1 \\n(.f -.el .ie \\*(f2 .ds f2 \\n(.f -.el .ie \\*(f3 .ds f3 \\n(.f -.el .ie \\*(f4 .ds f4 \\n(.f -.el .tm ? font overflow -.ft \\$1 -.. -.de fP -.ie !\\*(f4 \{\ -. ft \\*(f4 -. ds f4\" -' br \} -.el .ie !\\*(f3 \{\ -. ft \\*(f3 -. ds f3\" -' br \} -.el .ie !\\*(f2 \{\ -. ft \\*(f2 -. ds f2\" -' br \} -.el .ie !\\*(f1 \{\ -. ft \\*(f1 -. ds f1\" -' br \} -.el .tm ? font underflow -.. -.ds f1\" -.ds f2\" -.ds f3\" -.ds f4\" -'\" t -.ta 8n 16n 24n 32n 40n 48n 56n 64n 72n -.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 -\fBlong-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 -glimmer3 (1), -adjust (1), -anomaly (1), -build-icm (1), -check (1), -codon-usage (1), -compare-lists (1), -extract (1), -generate (1), -get-len (1), -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@pzr.uni-rostock.de for -the \fBDebian\fP system. - -...\" created by instant / docbook-to-man, Sun 09 Nov 2003, 19:43 diff --git a/debian/manpages.links b/debian/manpages.links deleted file mode 100644 index 57cc9f5..0000000 --- a/debian/manpages.links +++ /dev/null @@ -1 +0,0 @@ -tigr-glimmer glimmer2 diff --git a/debian/tigr-adjust.sgml b/debian/tigr-adjust.sgml deleted file mode 100644 index 8d11ab6..0000000 --- a/debian/tigr-adjust.sgml +++ /dev/null @@ -1,119 +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"> - - Novermber 10, 2004"> - 1"> - moeller@pzr.uni-rostock.de"> - - TIGR-GLIMMER"> - - - Debian"> - GNU"> - GPL"> -]> - - - -
- &dhemail; -
- - &dhfirstname; - &dhsurname; - - - 2003 - &dhusername; - - &dhdate; - - - &dhucpackage; - - &dhsection; - - - &dhpackage; - - -the program lacks a description - - - - - tigr-adjust - - - - DESCRIPTION - - - - - 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/tigr-check.sgml b/debian/tigr-check.sgml deleted file mode 100644 index 4106316..0000000 --- a/debian/tigr-check.sgml +++ /dev/null @@ -1,118 +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@pzr.uni-rostock.de"> - - TIGR-GLIMMER"> - - - Debian"> - GNU"> - GPL"> -]> - - - -
- &dhemail; -
- - &dhfirstname; - &dhsurname; - - - 2003 - &dhusername; - - &dhdate; - - - &dhucpackage; - - &dhsection; - - - &dhpackage; - - -The program lacks a description. - - - - - tigr-check - - - - DESCRIPTION - - - - - 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/tigr-codon-usage.sgml b/debian/tigr-codon-usage.sgml deleted file mode 100644 index 237c9eb..0000000 --- a/debian/tigr-codon-usage.sgml +++ /dev/null @@ -1,122 +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@pzr.uni-rostock.de"> - - TIGR-GLIMMER"> - - - Debian"> - GNU"> - GPL"> -]> - - - -
- &dhemail; -
- - &dhfirstname; - &dhsurname; - - - 2003 - &dhusername; - - &dhdate; - - - &dhucpackage; - - &dhsection; - - - &dhpackage; - - -The program lacks a description - - - - - tigr-codon-usage - - - - 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/tigr-compare-lists.sgml b/debian/tigr-compare-lists.sgml deleted file mode 100644 index 74e7b01..0000000 --- a/debian/tigr-compare-lists.sgml +++ /dev/null @@ -1,122 +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@pzr.uni-rostock.de"> - - TIGR-GLIMMER"> - - - Debian"> - GNU"> - GPL"> -]> - - - -
- &dhemail; -
- - &dhfirstname; - &dhsurname; - - - 2003 - &dhusername; - - &dhdate; - - - &dhucpackage; - - &dhsection; - - - &dhpackage; - - -unknown - - - - - tigr-compare-lists - - - - 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/tigr-generate.sgml b/debian/tigr-generate.sgml deleted file mode 100644 index 4b664a6..0000000 --- a/debian/tigr-generate.sgml +++ /dev/null @@ -1,118 +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@pzr.uni-rostock.de"> - - TIGR-GLIMMER"> - - - Debian"> - GNU"> - GPL"> -]> - - - -
- &dhemail; -
- - &dhfirstname; - &dhsurname; - - - 2003 - &dhusername; - - &dhdate; - - - &dhucpackage; - - &dhsection; - - - &dhpackage; - - -This program lacks a description. - - - - - tigr-generate - - - - DESCRIPTION - - - - - 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/tigr-get-len.sgml b/debian/tigr-get-len.sgml deleted file mode 100644 index 9c40308..0000000 --- a/debian/tigr-get-len.sgml +++ /dev/null @@ -1,118 +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@pzr.uni-rostock.de"> - - TIGR-GLIMMER"> - - - Debian"> - GNU"> - GPL"> -]> - - - -
- &dhemail; -
- - &dhfirstname; - &dhsurname; - - - 2003 - &dhusername; - - &dhdate; - - - &dhucpackage; - - &dhsection; - - - &dhpackage; - - -This program lacks a description. - - - - - tigr-get-len - - - - DESCRIPTION - - - - - 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/tigr-get-putative.sgml b/debian/tigr-get-putative.sgml deleted file mode 100644 index 8a5f0a0..0000000 --- a/debian/tigr-get-putative.sgml +++ /dev/null @@ -1,114 +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@pzr.uni-rostock.de"> - - TIGR-GLIMMER"> - - - Debian"> - GNU"> - GPL"> -]> - - - -
- &dhemail; -
- - &dhfirstname; - &dhsurname; - - - 2003 - &dhusername; - - &dhdate; - - - &dhucpackage; - - &dhsection; - - - &dhpackage; - - - - - - tigr-get-putative - - - - DESCRIPTION - - - 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. - - - - - -