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\sbasedon0\snext243 footer;}{\s244\tqc\tx4320\tqr\tx8640 \f20 \sbasedon0\snext244 header;}{\s253\li360 \b\f20\fs28 \sbasedon3\snext0 heading 3;}{\s254\sb120 \b\f21\fs28\cf1 \sbasedon3\snext0 heading 2;}{\s255\sb240 \b\f21\fs36\cf1 \sbasedon3\snext0
heading 1;}{\f20 \sbasedon222\snext0 Normal;}{\s2\li360 \f22\fs20 \sbasedon0\snext2 program;}{\s3 \f20 \sbasedon0\snext3 doc;}}{\info{\author Don Gilbert}}\widowctrl\ftnbj\fracwidth \sectd \sbknone\linemod0\linex0\cols1\endnhere {\header \pard\plain \s244
\brdrb\brdrs \tqr\tx8640 \f20 {\fs20 SeqApp Help\tab }{\fs20 {\field{\*\fldinst date \\@ "MMMM d, yyyy"}}}{\fs20 \par
}}{\footer \pard\plain \s243\qc\tqc\tx4320\tqr\tx8640 \f20 - \chpgn -\par
}\pard\plain \s3 \f20 {\fs20 \par
}{\fs28\ul SeqPup, version 0.6 development release, June/July 1996\par
}\pard\plain \f20 \par
{\b New in this release:\par
\par
}\tab Easily use GCG and other command-line software over network\par
\tab Bare-bones autosequencer (ABI,SCF) base calling, editing, assembly\par
\tab Expanded sequence size limits (now can open 1.9MB H.flu genome)\par
\tab Numerous bug fixes and improvements\par
\par
\pard\plain \s255\sb240 \b\f21\fs36\cf1 Summary{\par
}\pard\plain \s3 \f20 \par
SeqPup is a biological sequence editor and analysis program usable on the common computer systems including Macintosh, MS-Windows and X-Windows. It includes links to network services and external analysis programs.\par
\par
Features include\par
\pard \s3\tx440\tx720 \tab +\tab multiple sequence alignment and single sequence editing\par
\tab \tab read and write several sequence file formats \par
\tab +\tab easy hand alignment features including colored bases and sliding\par
\tab *\tab Internet sequence analysis services (e.g, GCG) by BOP and email methods \par
\tab *\tab automatic base calling from ABI or SCF trace files with autoseq app\par
\tab \tab automatic multiple sequence alignment with ClustalW app\par
\tab \tab automatic gel fragment alignment to contigs with CAP app\par
\tab \tab phylogenetic analysis of alignments with fastDNAml and LSADT apps\par
\tab \tab phylogenetic tree drawing with DrawTree and DrawGram Phylip apps\par
\tab \tab consensus, reverse, complement, degap, and distance/similarity operations \par
\tab \tab restriction maps\par
\tab +\tab pretty print of alignments and sequences with boxed and shaded regions\par
\tab \tab translate dna to/from protein using various codon tables\par
\tab +\tab find strings and ORFs\par
\tab \tab automatic preference saving\par
\tab \tab user-definable links to external analysis programs\par
\pard\plain \tx440\tx720 \f20 \tab \tab (* new, + updated)\par
\pard\plain \s3\tx720\tx1080 \f20 \par
\pard\plain \f20 NOTICE: This release is still unfinish, and has bugs. It may be useful to you as is, but be warned that it is still prone to problems.\par
\pard\plain \s3 \f20 \par
SeqPup is being written using DCLAP, a free and portable C++ class application framework. DCLAP is
founded on the NCBI Toolkit, especially it's Vibrant user-interface section written primarily by Jonathan Kans. SeqApp/SeqPup was started in 1990 as sequence editor/analysis platform on which analysis programs from other authors could be easily incorpora
ted into a useable interface. \par
\par
\pard\plain \f20 You can obtain this release thru anonymous ftp, gopher or http to iubio.bio.indiana.edu, in folder /molbio/seqpup. Versions are available for Macintosh (PowerMac and 68K), MS Windows (Win95, WinNT and Win3), and Unix/XWindows systems
including Sun Solaris, SGI Irix, DEC Unix, Linux. The Internet locators to this software are\par
\pard\plain \s3 \f20 \par
\pard \s3\li360 \par
\par
\par
\pard \s3 \par
Source code for this software is at .\par
\pard\plain \f20 The bopper source for installed a server for SeqPup Internet BOP functions is in this same folder as \par
\pard\plain \s3 \f20 \par
Comments, bug reports and suggestions for new features are very welcome and should be sent via e-mail to .\par
\par
\pard\plain \f20 {\ul June/July}{\ul 96:}{\ul version 0.6d }{\ul release}{\ul \par
}\pard \fi-360\li360 + "bopper" Internet protocol for client/server use of command line programs such as the GCG suite. \par
+ autoseq base calling app for reading ABI and SCF sequencer trace file data, plus base/trace editing functions.\par
+ Started expanding maximum sequence limit to 2 megabases (from about 30Kb), however most functions beyond viewing will still fail for >30Kb sequences.\par
+ Several bug fixes are included for mac, mswin, unix. Added background color in align view, minimum ORF size pref, improved tracking of changed data, improved align editing, save pretty print to PICT or text; fixed child app bugs;
fixed mswin edit truncation to 255 bases; editable data tables in selection dialogs\par
\pard \par
\page \par
\pard\plain \s255\sb240 \b\f21\fs36\cf1 SeqPup Help\par
\pard\plain \f20 \par
\pard\plain \s3\qc \f20 {\fs48 SeqPup \par
}{\fs28 version 0.6 development release\par
}\pard\plain \qc \f20 {\fs28 June/July 1996}{\par
}\pard \par
\pard\plain \s3 \f20 \par
SeqPup is a biological sequence editor and analysis program usable on the common computer systems including Macintosh, Motif/X-Windows and MS-Windows. It includes links to network services and external analysis programs.\par
\par
This program has already gone thru several changes since its start in September 1990. I don't expect it to mature for another year or two, as my prime programming time is holidays and weekends.\par
\par
Comments, bug reports and suggestions for new features (see below) are very welcome and should be sent via e-mail to\par
\par
\par
With any bug reports, I would appreciate as much detail as is reasonable without putting you off from making the report. If you don\rquote
t have time to send detailed descriptions of problems, please do send comments and reports, even if all you say is "Good" or "Bad" or "Ugly". \par
\par
Please include mention of computer hardware, and operating system software, including version. Describe how the problem may be repeated, if it is repeatable. If it is sporadic or only seen once, please also describe actions leading up to it. Include cop
ies of data if relevant.\par
\par
If you need to use land mail, send to\par
\par
\tab Don Gilbert\par
\tab Biocomputing Office, Biology Department\par
\tab Indiana University, Bloomington, IN 47405\par
\tab \par
\par
\par
\pard\plain \s255\sb240 \b\f21\fs36\cf1 Fetching\par
\pard\plain \s3 \f20 \par
You can obtain this software via Internet, using anonymous ftp, gopher or http to the IUBio server at iubio.bio.indiana.edu. It is located in folder /molbio/seqpup. Versions are available for Macintosh, MS Windows, and various XWindows/Unix systems. Ple
ase check the Readme files at this archive for recent news. Remember to use binary FTP to fetch the {\ul .zip }and {\ul .gz} binary files.\par
\par
Internet resource locators for this software are \par
\par
\par
\par
\par
\par
Source code for this software is at\par
\par
\par
You will need to fetch one of the program archive files for your computer system, its associated child app archive, and fetch the essential and optional items from the "all-systems" folder. For example, this would be\par
\par
\tab all-systems/ SeqPup.help, SeqPup.prefs, tables/*, seqs/*\par
plus\par
\tab mac/ seqpup-mac-68k.hqx and seqpup-mac-apps.hqx\par
or\par
\tab mswin/ seqpup16.zip and spapp1.zip\par
or\par
\tab unix/sun-sunos4-sparc/ SeqPup-sunos-mostat.gz and seqpup-apps.tar.gz\par
\par
\par
The current software distribution comprises the following items. \par
\par
\pard \s3\fi-3060\li3060\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920 all-systems/ mac/ mswin/ unix/\par
\par
all-systems/\par
SeqPup.help\tab \tab - help file (RTF format) {\b essential}\par
SeqPup-help.text \tab - help file (plain text)\tab {\i optional}\par
SeqPup.prefs\tab \tab - preferences file (plain text) {\b essential}\par
\par
tables/\tab \tab \tab - data files used by SeqPup, {\b essential}\par
codon.table\tab dro.cod\tab hum.cod\tab renzyme.table\par
color.table\tab eco.cod\tab rat.cod\tab tob.cod\par
\tab \par
appsrc/\tab \tab - source to applications called by SeqPup, {\i optional}\par
ChildApp.c\tab \tab captest.seq\tab \tab fastDNAml.doc\par
cap.src/\tab \tab clustalw.doc\tab \tab fastDNAml.infile\par
cap2.doc\tab \tab clustalw.src/\tab \tab fastdnaml.src/\par
\par
seqs/\tab \tab \tab - test sequence files, {\i optional}\par
23+28SrRNA.gb\tab captest.fasta\tab \tab fastdnaml.phylip\par
5srna.gb\tab \tab dros.ig\tab \tab \tab testre.map6\par
blue.seq\tab \tab ecolac.seq\tab \tab testreseq.gcg\par
\par
\par
mac:\tab \tab \tab - Macintosh, files are in binhex format\par
Readme \par
seqpup-mac-68k.hqx \tab - SeqPup for Mac with Motorola 68000 processor\par
seqpup-mac-ppc.hqx\tab \tab - SeqPup for Mac with PowerPC processor\par
seqpup-mac-apps.hqx\tab - child apps for mac, both 68k and PPC (fat binaries)\par
\par
mswin:\tab \tab - MS Windows, files are in ZIP archive binary format\par
Readme \par
seqpup16.zip \tab \tab - Seqpup for MS Windows, 16-bit code\par
seqpup32.zip \tab \tab - SeqPup for MS Windows, 32-bit code\par
spapp1.zip\tab \tab \tab - child apps for for mswin\par
\par
unix:\tab \tab \tab - Unix, files are in TAR, Gnu ZIP format\par
dec-alpha-osf/\tab \tab - DEC Alpha computer with OSF/1 Unix\par
linux-elf-i86/\tab \tab \tab - Linux OS, ELF binary format, Intel 80x86 processor\par
sun-sol2-i86/\tab \tab \tab - Sun Solaris 2 on Intel 80x86 processor\par
sun-sunos4-sparc/\tab \tab - Sun SunOS4 on SPARC processor (or Sol2)\par
sun-sol2-sparc/\tab \tab - Sun Solaris 2 on SPARC processor\par
sgi-irix/\tab \tab \tab - Silicon Graphics Iris\par
\par
unix/dec-alpha-osf:\tab \par
Readme SeqPup.gz seqpup-apps.tar.gz\par
\par
unix/sgi-irix:\par
Readme SeqPup.gz seqpup-apps.tar.gz\par
\par
unix/sun-sol2-i86:\par
Readme SeqPup.Z seqpup-apps.tar.Z\par
\par
unix/sun-sol2-sparc:\par
Readme SeqPup.gz seqpup-apps.tar.gz\par
\par
unix/sun-sunos4-sparc:\par
Readme\par
SeqPup-sunos-mostat.gz\tab - Motif libraries are included (will run on SunOS 4 or Solaris 2 lacking Motif libraries)\par
\pard \s3\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920 SeqPup-sunos-dyn.gz\tab - Motif libraries are not included\par
seqpup-apps.tar.gz\tab \tab - child apps for SPARC\par
\par
\par
\pard \s3 \par
\pard\plain \s255\sb240 \b\f21\fs36\cf1 Installing\par
\pard\plain \s3 \f20 \par
SeqPup is distributed over the Internet in archive files. The archive format used is commonly available on t
he computer system you use (HQX self-extracting for Macintosh, ZIP for MS Windows, and tar + Gnu ZIP for Unix). There is one primary program, several document and data files, examples, and child application programs. \par
\par
The current organization of files used by the program is:\par
\pard \s3\fi-2160\li2160\tx360\tx620\tx2340\tx2880\tx3600\tx4320 \tab SeqPup\tab -- execuable, called "seqpup.exe" in MSDOS\par
\tab SeqPup.help\tab -- this document, in Microsoft RTF format\par
\tab SeqPup.prefs\tab -- settings for the program, in text format.\par
\par
\tab tables/\tab -- data files, required for Restriction maps, translate and some other functions. These are standard bioinformatics data files available and updateable from various sources.\par
\tab \tab codon.table\tab -- table of codon preferences, in GCG format\par
\tab \tab renzyme.table\tab -- REBase data file, for restriction maps, in GCG format\par
\tab \tab color.table\tab -- table of color values for display of bases\par
\tab \tab hum.cod, tob.cod, eco.cod, and other codon preference tables that can substitute for codon.table at your preference\par
\par
\tab apps/\tab -- a selection of external analysis applications. \par
\tab \tab clustalw\tab -- multiple sequence alignment\par
\tab \tab cap2\tab -- contig alignment\par
\tab \tab fastDNAml\tab -- phylogenetic analysis of sequences\par
\tab \tab lsadt\tab -- De Soete Least Squares phylogeny analysis\par
\tab \tab drawtree\tab -- draw unrooted tree, from Phylip\par
\tab \tab drawgram\tab -- draw cladograms, from Phylip\par
\pard\plain \tx360\tx800\tx2340 \f20 \par
\pard\plain \s3\brdrt\brdrs \f20 {\i \par
Note for Sun systems: }
This program requires theMotif run-time libraries that are commonly found on other XWindow systems. Motif is not standard on SunOS and is not part of Solaris until verson 2.4. If you have Solaris 2.3 or earlier, or SunOS, and do not know that your sys
tem includes Motif, then you will need the version with statically bound Motif libraries (SeqPup-sunos-mostat.gz). \par
\par
\pard \s3
If you have Solaris 2.4, or a version where Motif libraries are present, you may still need to configure the system to let SeqPup know where they are. In a Solaris 2.4 system, where motif lives in /usr/dt/lib by default, this may be needed to run successf
ully:\par
\pard\plain \s2\li360 \f22\fs20 setenv LD_LIBRARY_PATH "$LD_LIBRARY_PATH":/usr/dt/lib\par
\par
\pard\plain \s3 \f20 If you get error messages with this saying something about an out-of-date library,\par
try instead putting the Motif /dt/lib in front:\par
\pard\plain \s2\li360 \f22\fs20 setenv LD_LIBRARY_PATH /usr/dt/lib:"$LD_LIBRARY_PATH"\par
\pard\plain \s3 \f20 \par
\pard\plain \brdrb\brdrs \tx360\tx800\tx2340 \f20 \par
\pard \tx360\tx800\tx2340 \par
\pard \par
\par
\pard\plain \s254\sb120 \b\f21\fs28\cf1 Installing preferences\par
\pard\plain \tx360\tx800\tx2340 \f20 \par
\pard\plain \s3 \f20
In addition to these two folders and three SeqPup files, the program will automatically create a personal preferences file in you computer when you first run it. These preferences come from the SeqPup.prefs file. The preferences file created on your sys
tem will be something like this\par
\pard \s3\tx720\tx5760 \tab System Folder:Preferences:seqpup.cnf\tab - MacOS \par
\tab c:\\windows\\seqpup.ini\tab - MS Windows \par
\tab ~/.seqpuprc\tab - Unix\par
\pard \s3 \par
The program will save various configuration information to this file. You may edit this with a text editor. You may delete it and a new one will be generated from the SeqPup.prefs file. You may not edit it while the program is active (any such changes ar
e lost). When the program is updated in the future, new preferences are added, using the label \par
\pard\plain \s2\li360 \f22\fs20 [version=123]\par
\pard\plain \s3 \f20 to indicate the version number.\par
\par
The preference file format is as follows:\par
\pard \s3\tx260 \tab - Logical sections are indicated in brackets [section].\par
\tab - Variables are denoted with a "name=value" format.\par
\tab - Line starting with ";" indicates a comment and will be ignored.\par
\pard \s3 \par
The current release of the program may require some fiddling to install correctly. This\par
is a known problem, and will be corrected in future releases. You will want to look at and probably edit the file "SeqPup.prefs". \par
\par
The following sections are important in getting the program to work right, and may need to be edited.\par
\pard\plain \s2\li360 \f22\fs20 [paths]\par
temp=\par
tables=tables\par
apps=apps\par
\par
[data]\par
codon=tables:codon.table\par
renzyme=tables:renzyme.table\par
color=tables:color.table\par
\pard\plain \f20 \par
\pard\plain \s3 \f20 If you use this on a Unix system or an MS DOS system, the current configuration should work if you start the program from its folder, e.g.,\par
\pard\plain \s2\li360 \f22\fs20 cd /path/to/seqpup/\par
./SeqPup\par
\par
\pard\plain \f20 A perhaps better way for Unix or MSDos systems is to set the environemntal variable called "SEQPUPHOME" to the path to SeqPup's folder, then you can run the program from any local directory (v.0.5 or 0.4k)\par
\pard\plain \s2\li360 \f22\fs20 \tab setenv SEQPUPHOME /path/to/seqpup/\par
\tab SeqPup\par
\pard\plain \f20 \par
\pard\plain \s3 \f20 But as is common on Unix, if you want to install this for use from any directory, you will currently need to edit the prefs file and put a fixed path to the SeqPup folders in it, as\par
\pard\plain \f20 \par
\pard\plain \s2\li360 \f22\fs20 [paths]\par
temp=/tmp\par
tables=/long/path/to/seqpup/tables\par
apps=/long/path/to/seqpup/apps\par
\pard\plain \f20 \par
\pard\plain \s3 \f20 If you run SeqPup first, then decide to change parts of the prefs file, you can have all users prefs be updated if you add the new prefs after a new version number. This is the procedure:\par
a) add a higher version number at the end of the SeqPup.prefs file\par
\pard\plain \s2\li360 \f22\fs20 [version=6]\par
{\plain \f22 \par
}\pard\plain \s3 \f20 b) add changed preference sections and values after that. You need not remove or edit the original values (I hope...).\par
\par
So for instance if the highest verson value in the prefs file is 5, then add this at the end of the SeqPup prefs to get all users preferences updated:\par
\pard\plain \f20 \par
\pard\plain \s2\li360 \f22\fs20 [version=6]\par
\par
[paths]\par
tables=/new/path/to/seqpup/tables\par
apps=/new/path/to/seqpup/apps\par
\pard\plain \f20 \par
\pard\plain \s3 \f20 {\i An important caveat with this}: New distributions of SeqPup will use new version values to trigger preference updates. If the new distribution has a lower version value than you have used, it won\rquote t trigger an update.
\par
\par
Child applications are configured for use with the SeqPup.prefs file. Please see below the section {\b Child Tasks.}\par
\pard\plain \f20 \par
\par
\par
\pard\plain \s255\sb240 \b\f21\fs36\cf1 Source code and DCLAP\par
\pard\plain \s3 \f20 \par
SeqPup is built on an object-oriented application framework, written in C++, called DCLAP. This framework is designed to speed the development of easy to use, complex programs with a rich user-interface. At this point, DCLAP is still an unfinished framew
ork, lacking in documentation. However, it is rich enough at this point to build complex programs like SeqPup. \par
\par
\pard \s3\fi-1440\li1440\tx260\tx1160 DCLAP includes the following segments\par
\tab DClap/\tab -- basic application framework, including command, control, dialog, file, icon, list, menu, display panel, table view, mouse tracker, child application, window and view classes.\par
\tab Drtf/\tab -- rich text display handlers, including RTF, HTML document, PICT and GIF image format readers.\par
\tab DNet/\tab -- Internet connection tools, including TCP/IP, SMTP, Gopher and preliminary HTTP classes.\par
\tab DBio/\tab -- Biocomputing methods, included biosequence, restrict enzyme, sequence editor, seq. manipulator, seq. output classes. \par
\pard \s3 \par
New applications can be built to employ and reuse these classes fairly quickly. Variations on the current methods are simple to add in the class derivation method of C++. For instance, new document formats can be added on the Drtf display objects, and n
ew sequence manipulations can be added in the biosequence handlers, by building on current methods.\par
\par
DCLAP rests upon the NCBI toolkit, including the Vibrant GUI toolkit, which is designed for cross-platform functioning. The successful genome data browser Entrez is written with the NCBI toolkit. \par
\par
All of this source is available without charge for non-profit use (see copyright below). The NCBI toolkit portion is further available for profit use, and such arrangements may be made for use of DCLAP.\par
\par
DCLAP will never compete with commercial programming frameworks, but it has the virtue of being freely available and redistributable, an
d includes support specifically for biocomputing applications. If you are undertaking a biocomputing project requiring a rich user interface, and wish it to run on multiple computer platforms, this may be a worthwhile choice, especially if you wish to red
istribute your source code for the benefit of the scientific community. \par
\par
The DCLAP developer archive is at \par
Please contact Don Gilbert for further information on using this framework in other applications.\par
\par
\par
\par
\pard\plain \s255\sb240 \b\f21\fs36\cf1 Copyright\par
\pard\plain \s3 \f20 \par
This SeqPup program is Copyright (C) 1990-1996 by D.G. Gilbert. \par
All Rights are reserved.\par
\par
gilbertd@bio.indiana.edu \par
Biology Dept., Indiana University, Bloomington, IN 47405 \par
\par
You may use this program for your personal use, to provide a non-profit service to others.\par
You may not use this program in a commercial product, nor to provide commercial service, nor may you sell this code without express written permission of the author. \par
You may redistribute this program freely. If you wish to redistribute it as part of a commercial collection or venture, you need to contact the author for permission. \par
\par
The source code to this program is likewise copyrighted, and may be used, modified and redistributed in a free manner. Commercial uses of it need prior permission of the author. \par
\par
Any external applications that may distributed with SeqPup are copyrighted by their respective authors and subject to distribution provisions as described by those authors. At present this includes ClustalW, by Des Higgin
s, CAP2 by Xiaoqiu Huang, and FastDNAml, written by Joseph Felsenstein with modifications by Gary Olsen, Hideo Matsuda and Ross Overbeek, is copyrighted by University of Washington and\par
Joseph Felsenstein.\par
\par
Distribution of external analysis applications with this program is done as a convenience for users, and in no way modifies the original copyright. If there is a problem with this, instructions to users for obtaining and installing external applications w
ill be substituted.\par
\par
No warranty, express or implied, is provided with this software. The author is trying to produce a good quality program, and will incorporate corrections to problems reported by users of it.\par
\pard\plain \f20 \par
\pard\plain \s3 \f20 \par
\pard\plain \s255\sb240 \b\f21\fs36\cf1 Views\par
\pard\plain \s3 \f20 \par
There are four main types of views or displays in SeqPup:\par
\par
A multiple-sequence view which is the primary display when you open a sequence document; the single sequence editting view; various print views which result from an analysis, like the Restriction map; and dialog views where you control some function.
\par
\par
Many of these views have dialog controls -- push buttons, check boxes, radio controls and edittable text items -- to let you fine-tune a view to fit your preference. Many of these views also will remember your last preferences.\par
\par
When a view has editable text items, including the sequence entry views, most usual undo/cut/copy/paste features will work. \par
\par
Two or more views of the same data are possible. Some of these are truly views of the same data -- changes made in one view are reflected in another. Other views are static pict
ures taken of the data at the time the analysis was performed -- later changes to the data do not affect that picture.\par
\par
\pard\plain \s254\sb120 \b\f21\fs28\cf1 Aligned multi-sequence view\par
\pard\plain \s3 \f20 \par
The main view into a sequence document is the multiple sequence editor window, which lists sequence names to the left and sequence bases as one line that can be scrolled thru. Bases can be colored (now only nucleic colorings) or black. Sequence can be ed
itted here, especially to align them, and subranges and subgroupings can be selected for further oper
ations or analysis. Entire sequence(s) can be cut/copied/pasted by selecting the left name(s). Mouse-down selects one. Shift-mouse down selects many in group, Command-mouse down selects many unconnected. Double click name to open single sequence view. Se
lect name, then grab and move up or down to relocate.\par
\par
Select the lock/unlock button at the view top to lock/unlock text editting in the sequence line. With lock on (no editting) you can use shift and command mouse to select a subrange of sequences to operate on.\par
\par
Bases can be slid to left and right, like beads on an abacus, when the edit lock is On (now default). Select a base or group of bases (over one or several sequences), using mouse, shift+mouse, option+mouse, command+mouse. Then grab selected bases with mo
use (mouse up, then mouse down on selection), and slide to left or right. Indels "-" or spacing on ends "." will be added and squeezed out as needed to slide the bases. See also the "Degap" menu selection to remove all gaps thus entered from a sequence.
\par
\par
\pard\plain \s254\sb120 \b\f21\fs28\cf1 Single sequence view\par
\pard\plain \s3 \f20 \par
For entering/editting a single sequence, this view displays one sequence with more info and control. Edit the name here (later other documentation). Bring out this view by double-clicking sequence name in align view, or choosing Edit from Sequence menu.
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\pard\plain \s254\sb120 \b\f21\fs28\cf1 Print views\par
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Various analyses provide non-editable displays. These are usually save-able as PICT format for editting in your favorite MacDraw program, or print-able.\par
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\pard\plain \s255\sb240 \b\f21\fs36\cf1 Data files\par
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SeqPup uses plain TEXT type fi
les for its primary sequence data. These files can be exchanged without modification with many other sequence analysis programs. SeqPup automatically determines the sequence format of a data file when openning it. You have an choice of several formats
to save it as. As of this writing, the GenBank format is prefered (see bugs).\par
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The program looks in the folder "tables" for text files containing various data. At present these files include "codon.table", "renzyme.table" and "color.table".\par
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There is a "SeqPup.prefs" file which stores various user options like window positions, mail address, child tasks. This is described more in the Install and Child Apps sections.\par
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Various temporary files are created for child tasks, generally in the :Apps: folder. Currently you cannot run the Child Tasks portion of SeqPup from a locked file server because these temporary files need to be created where the child applications reside.
Otherwise, SeqPup should operate from a locked fileserver properly, and can be launched by several users at once.\par
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\pard\plain \s254\sb120 \b\f21\fs28\cf1 Restriction Enzyme Table\par
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The file called "renzyme.table" contains restriction enzyme data, as distributed in REBASE by R.Roberts. The format used is identical to that used by GCG software.\par
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\pard\plain \f20 {\fs18 \tab \{ documentation ...\}\par
\tab \par
Commercial sources of restriction enzymes are abbreviated as follows:\par
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\tab \tab A\tab Amersham (12/91)\par
\tab \tab B\tab BRL (6/91)\par
\tab \tab ...\par
\tab \tab X\tab New York Biolabs (4/91)\par
\tab \tab Y\tab P.C. Bio (9/91)\par
\par
.. \{< separates data\}\par
;AatI 3 AGG'CCT 0 ! Eco147I,StuI >OU\par
AatII 5 G_ACGT'C -4 ! >EJLMNOPRSUVX\par
AccI 2 GT'mk_AC 2 ! >ABDEIJKLMNOPQRSUVXY\par
;AccII 2 CG'CG 0 ! Bsp50I,BstUI,MvnI,ThaI >DEJKQVXY\par
;AccIII 1 T'CCGG_A 4 ! BseAI,BsiMI,Bsp13I,BspEI,Kpn2I,MroI >DEJKQRVY\par
;Acc65I 1 G'GTAC_C 4 ! Asp718I,KpnI >DFNY\par
}\par
\pard\plain \s3 \f20 \par
\pard\plain \s254\sb120 \b\f21\fs28\cf1 Codon Table\par
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The file called "codon.table" in folder "Tables" is used for translation of nucleic to protein seque
nce, and for backtranslation. This file may be replaced with a table of your choice in the following format (this format is identical to that used by GCG software codon tables).\par
\pard\plain \f20 \par
{\fs20 \tab \{ any documentation... \}\par
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AmAcid Codon Number /1000 Fraction .. \{< data separator\}\par
Gly GGG 1743.00 9.38 0.13\par
Gly GGA 1290.00 6.94 0.09\par
... \{ continue for 64 codons \}}\par
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\pard\plain \s255\sb240 \b\f21\fs36\cf1 Features\par
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The following topics describe main features found in the SeqPup menus.\par
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\pard\plain \s254\sb120 \b\f21\fs28\cf1 File \par
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{\b New} will create an align view of sequence data. New Text will create a plain text document, which is the format of the sequence data files also. \par
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{\b Open} will open an exising file. The default choice will open a file of sequences into a new window. You can choose "Sequence, append", or hold down the SHIFT key, to open a sequence file and append it to an existing alignment window.\par
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Other {\b Open} options include opening a plain text file, a file of phylogeny trees in Newick format (see Phylip documentation), or a Gopher document.\par
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{\b Save}, Save as, Save a copy in, all will save the current document to disk files. Revert will restore the open align view to the last version saved to disk.\par
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{\b Save selection}, Saves only highlighted sequences to a new disk file. Doesn\rquote t affect save status of current full alignment document.\par
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{\b Print} setup, print will print the current view.\par
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{\b Help} brings up a view to page thru the help file.\par
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{\b Preferences} will set some user preferences. \par
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\pard\plain \s254\sb120 \b\f21\fs28\cf1 Editing\par
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{\b Undo}, {\b cut}, {\b copy}, {\b paste}, {\b clear}, {\b select} {\b all} -- these standard mac commands will operate on text as well as on sequences in (hopefully) intuitive, usual ways.\par
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{\b Find}, Find same, Find "selection" will search for strings in text.\par
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{\b Replace}, replace same will replace target strings (not yet enabled).\par
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\pard\plain \s254\sb120 \b\f21\fs28\cf1 Sequence manipulations\par
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{\b New sequence} -- append a new, blank sequence to the sequence document.\par
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{\b Edit} -- open single sequence editting view for selected items.\par
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{\b Reverse}, {\b Complement}, {\b Rev-complement }-- Reverse, complement or reverse+complement a sequence. Works on one or more sequences, and the selected subrange.\par
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{\b Rna-Dna,Dna-Rna} -- Convert dna to rna (t->u) and vice versa. Works on one or more sequences, and the selected subrange.\par
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{\b Degap} -- remove alignment gaps "~". Works on one or more sequences, and the selected subrange. Gaps of "-" are locked and not affected by Degap. Works on one or more sequences, and the selected subrange.\par
{\b \par
Lock Indel & Unlock Indel} -- Convert from unlocked gaps "~", to locked gaps "-". Unlocked gaps will disappear and appear as need
ed as you slide bases left and right. Locked gaps are not affected by sliding nor by Degap. Works on one or more sequences, and the selected subrange.\par
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{\b Consensus} -- generate a consensus sequence of the selected sequences.\par
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{\b Translate} -- translate to/from amino acid. Relies on Codon.Table data.\par
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{\b Pretty print} -- a prettier view of a single or aligned sequences. Use these views to print your sequences. Printing from the editing display will not be supported fully, and may not print all of your sequence(s).\par
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{\b Restriction map} -- Restriction enzyme cut points of selected sequence. Also protein translation options.\par
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{\b Dotty plot} -- provide a dot plot comparison of two sequences. \par
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{\b Nucleic, amino codes} -- These provide both reminders of the base codes, and a way to select colors to assocate with each code (new in v 1.9a). See below for some discussion of the two "aa-color" documents that now ship with SeqPup. \par
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\pard\plain \s255\sb240 \b\f21\fs36\cf1 Child Tasks\par
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The "ChildApps" menu lets you link SeqPup with external sequence analysis programs
that you or others may write. SeqPup can be configured to launch any other application, and to send it sequence data and command information. When the child program is finished with its analysis, SeqPup can open and display results files from the child
in a variety of formats, including text, biosequence, PICT, RTF and GIF. On Macs, the ChildApps menu requires System 7 to operate.\par
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The general design of child applications is taken to be data analysis programs that have a simple command-line user-interfa
ce, and that take input data from a file or from the system "standard input" file (stdin), and that write outputs to files and to two system standard files "standard output" (stdout) and "standard error" (stderr). This is how many existing analyses progra
ms work, and it is very straightforward to program this basic kind of user-interface. \par
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The value of SeqPup joined with these kinds of programs is that the SeqPup can concentrate on providing an easy-to-use interface for biologists, and the analysis appli
cation can concentrate on data analyses, without having to add a lot of software baggage to provide a more usable interface.\par
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A desired addition to SeqPup will be a dialog to configure new and current child tasks. However, at present this needs to be done by using a text editor to change the SeqPup.prefs file.\par
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\pard\plain \s254\sb120 \b\f21\fs28\cf1 Configuring child applications\par
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You can add new child apps by editing the text file SeqPup.prefs. You will need to update the section [apps] with a new line for you new app, then install a new
section, [newappname]. You will also need to increase the [version=#] value, as described above in the {\b Installation} section, for the program to take notice of your changes.\par
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The [apps] section contains a list of child app sections, and the menu title string. E.g.,\par
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\pard\plain \s2\li360 \f22\fs20 [apps]\par
clustal=ClustalW Multiple align...\par
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The clustal= line says there is a child app section called clustal, and its menu title is "ClustalW Multiple align..."\par
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Version 0.5 adds the {\b form=path-to-html-form} method for configuring child apps.\par
Forms are the recommended replacement to the following methods. This new feature needs documenting, but is still evolving. It follows the HTML forms standard, though not all HTML specs are implemented at this release. \par
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See the example HTML forms in the {\b apps} folder to find how these work.\par
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The following variable names have special meaning as Input tags of {\ul TYPE=hidden}:\par
\pard \s3\li360 infile, seqformat, minseq, maxseq\par
outfile1, outfile2, .. outfile{\i n}\par
stdin, stdout, stderr, stdcmdin \par
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\pard \s3 The HTML