Author: moeller Date: 2010-07-11 05:11:55 +0000 (Sun, 11 Jul 2010) New Revision: 5032
Added: trunk/packages/acedb/trunk/debian/dotter.1 trunk/packages/acedb/trunk/debian/efetch.1 Log: Who did not check in my newly created man pages? Added: trunk/packages/acedb/trunk/debian/dotter.1 =================================================================== --- trunk/packages/acedb/trunk/debian/dotter.1 (rev 0) +++ trunk/packages/acedb/trunk/debian/dotter.1 2010-07-11 05:11:55 UTC (rev 5032) @@ -0,0 +1,79 @@ +.\" This file was generated by help2man 1.37.1 and then manually edited. +.TH DOTTER: "1" "July 2010" +.SH NAME +dotter \- Sequence dotplots with image enhancement tools. +.SH SYNOPSIS +dotter [options] <horizontal_sequence> <vertical_sequence> [X options] +.SH DESCRIPTION +.IP +Reference: Sonnhammer ELL & Durbin R (1995). A dot\-matrix program +with dynamic threshold control suited for genomic DNA and protein +sequence analysis. Gene 167(2):GC1\-10. +.TP +.TP +Allowed types: +Protein \- Protein +DNA \- DNA +DNA \- Protein +.IP +Options: +.TP +\fB\-b\fR <file> +Batch mode, write dotplot to <file> +.TP +\fB\-l\fR <file> +Load dotplot from <file> +.TP +\fB\-m\fR <float> +Memory usage limit in Mb (default 0.5) +.TP +\fB\-z\fR <int> +Set zoom (compression) factor +.TP +\fB\-p\fR <int> +Set pixel factor manually (ratio pixelvalue/score) +.TP +\fB\-W\fR <int> +Set sliding window size. (K => Karlin/Altschul estimate) +.TP +\fB\-M\fR <file> +Read in score matrix from <file> (Blast format; Default: Blosum62). +.TP +\fB\-F\fR <file> +Read in sequences and data from <file> (replaces sequencefiles). +.TP +\fB\-f\fR <file> +Read feature segments from <file> +.TP +\fB\-H\fR +Do not calculate dotplot at startup. +.TP +\fB\-R\fR +Reversed Greyramp tool at start. +.TP +\fB\-r\fR +Reverse and complement horizontal_sequence (DNA vs Protein) +.TP +\fB\-D\fR +Don't display mirror image in self comparisons +.TP +\fB\-w\fR +For DNA: horizontal_sequence top strand only (Watson) +.TP +\fB\-c\fR +For DNA: horizontal_sequence bottom strand only (Crick) +.TP +\fB\-q\fR <int> +Horizontal_sequence offset +.TP +\fB\-s\fR <int> +Vertical_sequence offset +.IP +Some X options: +\fB\-acefont\fR <font> Main font. +\fB\-font\fR <font> Menu font. +.SH SEE ALSO +http://www.cgb.ki.se/cgb/groups/sonnhammer/Dotter.html for more info. +.SH AUTHOR [email protected] +Version 3.1, compiled Jul 10 2010 Added: trunk/packages/acedb/trunk/debian/efetch.1 =================================================================== --- trunk/packages/acedb/trunk/debian/efetch.1 (rev 0) +++ trunk/packages/acedb/trunk/debian/efetch.1 2010-07-11 05:11:55 UTC (rev 5032) @@ -0,0 +1,95 @@ +.\" This file was generated by help2man 1.37.1 with some additional +.\" manual editing. +.TH EFETCH "1" "July 2010" +.SH NAME +efetch \- retrieve entries from sequence databases. +.SH SYNOPSIS +efetch \fB\-options\fR [database:]<query> +.SH DESCRIPTION +In the late 90s efetch was a very popular tool to extremely quickly retrieve +entried from the most common public bioinformatics sequence and motif databases. +We will learn from the Debian and Ubuntu popularity contest effort if the +package is possibly gaining a larger userbase again. +.SH DATABASES +SWissprot/SP, PIR, WOrmpep/WP, EMbl, GEnbank/GB, ProDom, ProSite +.SH OPTIONS: +\fB\-a\fR Search with Accession number +.HP +\fB\-f\fR Fasta format output +.HP +\fB\-q\fR Sequence only output (one line) +.HP +\fB\-s\fR <#> Start at position # +.HP +\fB\-e\fR <#> Stop at position # +.HP +\fB\-o\fR More options and info... +.HP +\fB\-D\fR <dir> +Specify database directory +.HP +\fB\-H\fR +Display index header data +.HP +\fB\-p\fR +Display entrynames in search path +.HP +\fB\-r\fR +Print sequence in 'raw' format +.HP +\fB\-m\fR +Fetch from mixed mini database +.HP +\fB\-M\fR +Mini format output +.HP +\fB\-b\fR +Do NOT reverse the order of bytes +(SunOS, IRIX do reverse, Alpha not) +.HP +\fB\-d\fR <dbfile> +Specify database file (avoid this) +.HP +\fB\-i\fR <idxfile> +Specify index file (avoid this) +.HP +\fB\-l\fR <divfile> +Specify division lookup table (avoid this) +.HP +\fB\-B\fR <database> Specify database (archaic) +.HP +\fB\-A\fR +Only return entryname for accession number +.HP +\fB\-n\fR <name> +Give the sequence this name +.HP +\fB\-x\fR +Don't require query to match entry's name exactly (avoid) +.HP +\fB\-w\fR +For Wormpep: also fetch cross\-referenced SwissProt entry +.HP +\fB\-h\fR +shows this help text +.SH ENVIRONMENT +SWDIR = SwissProt directory \- database and EMBL index files +PIRDIR = PIR \fB\-\-\fR " \fB\-\-\fR +WORMDIR = Wormpep \fB\-\-\fR " \fB\-\-\fR +EMBLDIR = EMBL \fB\-\-\fR " \fB\-\-\fR +GBDIR = Genbank \fB\-\-\fR " \fB\-\-\fR +PRODOMDIR = ProDom \fB\-\-\fR " \fB\-\-\fR +PROSITEDIR = ProSite \fB\-\-\fR " \fB\-\-\fR +DBDIR = User's own \fB\-\-\fR " \fB\-\-\fR (fasta format) +.TP +SEQDB +database file (default SwissProt) +.IP +SEQDBIDX index file +DIVTABL division lookup table +.IP +Ex. setenv DBDIR /pubseq/seqlibs/embl/ +.IP +Note that Prodom family consensus seqs can be fetched by PD:_# +.SH AUTHOR +Erik Sonnhammer ([email protected]) _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
