Celestin Apprentice 5/Apprentice-Release5.iso/Source Code/Libraries/DCLAP 6d/dclap6d/Docs/SeqPup.Help

Text File | 1996-07-05 | 22KB | 612 lines

SeqPup Help
                            -  -
@Abstract

SeqPup is a biological sequence editor and analysis program
for Macintosh computers.  It includes links to network
services and  external analysis programs.

Features include
     multiple sequence alignment editor
     single sequence editor window
     read and write several sequence file formats
     consensus,reverse,complement,degap operations
     automatic preference saving
     internet send mail
     internet sequence analysis services
     and more


NOTICE:  This is an early, unfinished version of the
program.   Expect it to fail in various ways.  This release
is made available to those who wish to test and comment on
its future development. This release will expire on a date
indicated in the About dialog.

SeqPup is being written by Don Gilbert using DCLAP, a C++
Class Application framework, and founded on the NCBI
Toolkit, especially it's Vibrant user-interface section
written by Jonathan Kans.   DCLAP is based loosely on the
MacApp extensible programming framework from Apple Computer.

You can obtain updates of this release thru anonymous ftp to
ftp.bio.indiana.edu, in folder /molbio/seqpup, as seqpup.hqx
(Macintosh), seqpup.zip (MS Windows), seqpup-sun-sparc.tar.Z
(SunOS Sparcstation), and perhaps other binaries. There may
be additional distribution software, data or information in
this /molbio/seqpup folder.  See the Readme files in it for
details.

The file SeqPup.Help is a plain text file which may be read
from your favorite wordprocessor or from the Edit program in
the Apps folder.  If you have problems getting SeqPup to
launch, and cannot  read this help from SeqPup, please read
it with another application  to help solve the problem.

Comments, bug reports and suggestions for new features (see
below) may be addressed via e-mail to

          [e-mail]

History

SeqPup was started Sept. 1990 as MacApp sequence
editor/analysis platform  on which analysis programs from
other authors, typically command line  w/ weak user
interfaces, could be easily incorporated into a useable Mac
interface.


@SeqPup Help

SeqPup provides a biological sequence editor and related
functions, including links to network services and external
analysis programs.

  *******************************************
  ****                    NOTICE
  ****
  ****  This is an early, unfinished version of the
  ****  program.  Expect it to fail in various ways.
  ****  This release made available to those who wish
  ****  to test and comment on its future development.
  ****
  *******************************************

This program is a long-term research/development project.
It has already gone thru several changes since its start in
September 1990.  Don't expect it to be "complete" for a
while (years) yet.  It is publicly available now as it has
been useful to some as is.

Comments, bug reports and suggestions for new features (see
below) may be addressed via e-mail to
          [e-mail]

With any bug reports, I would appreciate as much detail as
is reasonable without putting you off from making the
report.  Include description of computer hardware, system
software version.  Include copies of data if relevant.

If you need to use land mail, send to

               Don Gilbert
               Biocomputing Office, Biology Department
               Indiana University, Bloomington, IN 47405

This SeqPup program is copyrighted 1992 by D.G. Gilbert.  It
is written using DCLAP, a C++ Class Application framework,
also developed by D.Gilbert.  This framework is founded on
the NCBI Toolkit, especially it's Vibrant user-interface
section written by Jonathan Kans.   DCLAP is based loosely
on the MacApp extensible programming framework from Apple
Computer.

Any external applications that may distributed with SeqPup
are copyrighted by their respective authors and subject to
distribution provisions as described by those authors.


@Installing

[--- obsolete --- needs rewriting for SeqPup --- ]


@Views

There are now four main types of views or displays in
SeqPup:

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.

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.

When a view has edittable text items, including the sequence
entry views, most usual Mac undo/cut/copy/paste features
will work, as will font, size and style controls.

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
pictures taken of the data at the time the  analysis was
performed -- later changes to the data do not affect that
picture.

@@Aligned multi-sequence view

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 editted here, especially to align
them, and subranges and subgroupings can be selected for
further operations 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.  Select name, then grab and move
up or down to relocate.

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.

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 mouse (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.

@@Single sequence view

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.

@@Print views

Various analyses provide non-editable displays.  These are
usually save-able as PICT format for editting in your
favorite MacDraw program, or print-able.

@Data files

SeqPup uses plain TEXT type files 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).


There is a "seqpup.cnf" (mac) / "seqpup.ini" (mswin) /
".seqpuprc" (unix) file which stores various user options
like window positions, mail address, child tasks.  Also look
for "dclap..." prefs file.  This automatically generated by
SeqPup.  It goes in a System Folder:Preferences: folder
(mac) .




@Features

The following topics describe main features found in the
SeqPup menus.

@@File

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.

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.

Other Open options include opening a plain text file, a file
of phylogeny trees in Newick format (see  Phylip
documentation), or a Gopher document.

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.

Save selection, Saves only highlighted sequences to a new
disk file.  Doesn't affect save status of current full
alignment document.

Print setup, print will print the current view.

Help brings up a view to page thru the help file.

Preferences will set some user preferences.

@@Editing

Undo, cut, copy, paste, clear, select all -- these standard
mac commands will operate on text as well as on sequences in
(hopefully) intuitive, usual ways.

Find, Find same, Find "selection" will search for strings in
text.

Replace, replace same will replace target strings (not yet
enabled).


@@Sequence manipulations

New sequence -- append a new, blank sequence to the sequence
document.

Edit -- open single sequence editting view for selected
items.

Reverse, Complement, Rev-complement -- Reverse, complement
or reverse+complement a sequence. Works on one or more
sequences, and the selected subrange.

Rna-Dna,Dna-Rna -- Convert dna to rna (t->u) and vice versa.
Works on one or more sequences, and the selected subrange.

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.

Lock Indel & Unlock Indel -- Convert from unlocked gaps "~",
to locked gaps "-".  Unlocked gaps will disappear and appear
as needed 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.

Consensus -- generate a consensus sequence of the selected
sequences.

Translate -- translate to/from amino acid.  Relies on
Codon.Table data.

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).

Restriction map -- Restriction enzyme cut points of selected
sequence.  Also protein translation options.

Dotty plot -- provide a dot plot comparison of two
sequences.

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.

@@Internet

The Internet features of SeqPup let you interchange ideas
and data with people and biocomputing services around the
world.  If your Mac is connected already to the Internet,
you probably are familiar with electronic mail and some of
its uses.

SeqPup includes a selection of network access features in
the developing area of networked biocomputing.  You will
find access to me, at least to get comments and bug reports
to me, very easy.  There is a feature to send and receive e-
mail, as well as mail links to customized e-mail services.
These include searching for sequence similarity via BLAST
and FastA programs on the Genbank/Intelligenetics computers,
fetching sequences, data and software from Genbank and EMBL.

There is now an feature called Gopher, which gives you
access to a wide range of information services now
developing on the Internet.  Gopher is something like Telnet
or FTP (file transfer), but also different.  It includes
some of the keyword searching features of WAIS (Wide Area
Information Services). There are currently several biology
gopher services found around the globe. These include fast
and up-to-date keyword searches of GenBank, EMBL, PIR and
other important biology databanks.



@@@Mail Preferences

The mail prefs dialog asks for your return e-mail address,
your preferred SMTP mail host, and your POP mail address and
password.  These addresses may be similar.

Return e-mail address:  This is where another person should
send mail so it will reach you.
          Example:  [e-mail]
                  or:  [e-mail]

SMTP Mail host:  This is the internet address of the
computer thru which  SeqPup will send out mail to the rest
of the world.
          Example:  MainComputer.University.Edu


@@@Send Mail

Send an electronic mail message.  You must enter an address
to send to, and have entered your return address in the mail
preferences dialog.


@Mail-based Search and Fetch

Various network resources provide biocomputing services thru
e-mail.  These include retreiving sequence entries from the
various databanks (GenBank, EMBL, PIR), fetching help
documents, and searching for sequences in the databanks that
match your query sequences.




@Bugs

SeqPup version -1 has plenty of bugs and missing features,
including:

     no Undo (this is a real bite to those used to it)
     mostly no cut/copy/paste/clear
     limited printing of documents or views
     mostly no align-view manipulations (move,cut/copy,edit
in place, shift, ...)
     no pretty print views
     no restriction maps
     no dot plots
     no ...
     problems w/ window display & keeping track of active
window (x,mswin)

I'll be adding back many of these features from the
Macintosh SeqApp as time permits.


SeqApp version 1.9a involved major amounts of rewriting of
the underlying program code, without as many improvements as
I would have liked.   This major rewrite was prompted by the
move from Apple's extensible macintosh application
framework, MacApp version 2 to version 3.  The move was
needed because MacApp 2 is essentially obsolete.  New
general application features are found in MacApp version 3,
a few of which you may notice.  Also, this is preliminary to
translating the code from the Object Pascal language into
the C++ language.  The future of MacApp is to move to a
computer-make independent application framework called
Bedrock, which may be available in 1994 for Mac, Windows,
and possibly Unix systems.  It is my hope to move SeqPup
onto this, but I make no promises or predictions at this
time.

There are still several known bugs, and probably some
unknown bugs lurking in this release.   A prime rule in
using this software is to be aware of its incomplete nature,
and save early and often.

Please also send in detailed descriptions of bugs you find.
If the bug seems to be erratic, as many are, try to find
some circumstances which will cause it to appear repeatable
and explain these to me.   Your reports will help improve
this program for you and others.  E-mail bug reports to
     [e-mail]



@Future Features


The future of MacApp on which SeqApp is based, is to move to
a platform independent application framework called Bedrock,
which may be available in 1994 for Mac, Windows, and
possibly Unix systems.  It is my hope to move SeqPup onto
this, but I make no promises or predictions at this time.

[Winter 1994:  The future is here -- BedRock is dead, but
DClap is here instead to provide a platform independent
framework.]

Here is a list of things which may be added to SeqPup in the
future, depending on your interest.

Sequence documentation handling.  Currently no provisions
for documentation per sequence.  This will at least change
to a window for any comments and saving it into files (where
file format permits).  Possibly I will put effort into
dealing with the features, references, etc., in a fashion
along lines of Genbank/EMBL documentation structure &/or
Authorin documentation. Your comments on the importance of
this are desired.

Feature table parsing -- pull out subsequences from Gen/EMBL
feature info.

Align, single sequence pretty print -- header, page
numbering user prefs should be added.

Restriction map -- Could use some speed-up.  Some would like
graphic map (i.e., one line or circle w/ cut points per
zyme).

NCBI ASN.1 file format. -- this will be available soon after
the 1.9a 157 release, as the newest Readseq code which
reads/writes ASN.1, is fully rolled into SeqPup.

Open reading frame mapping, other single sequence analyses (
what?)

Simple protein analysis routines, better protein handling
(colors are now nuc specific).  -- colors are user
selectable now in 1.9a.   I expect to put most/all of the
features of DNA Strider into SeqPup -- let me know your
favorite ones.

Links to child tasks:  these depend as much on agreement of
the authors of various routines as on user interest.  Among
routines that I already have a handle on -- MulFold (Zuker),
Phylip phylogeny analysis (Felsenstein), tree draw program
(Felsenstein + my hacks a la Tree Draw desk).

Links to NETWORKED child tasks (e.g., on fast compute
servers).   Perhaps thru Gopher, or otherwise.


@History

SeqPup/SeqApp was started Sept. 1990 as MacApp sequence
editor/analysis platform  on which analysis programs from
other authors, typically command line with weak user
interfaces, could be easily incorporated into a useable Mac
interface.

SeqPup, March 1994, version -1.  First public release of
SeqPup, the platform-independent version derived from the
earlier Macintosh SeqApp.  SeqPup will eventually include
most or all of SeqApp's features, and new features will be
added.

SeqApp, 20 June 93, version 1.9a162 -- a minor update, with
these bug fixes since last release:
  -- fixed base number index in align view to correctly
index the bases.  Also fixed base number index scrolling
link to sequence scrolling.
  -- fixed paste of align sequence into blank window to
correctly update full width of display.

12+ June 93, version 1.9a157+ -- a semi-major update, and
time extension release with various enhancements and
corrections.  These include
  -- lock/unlock indels (alignment gaps). Useful when
sliding bases around
  during hand alignment, to keep alignment fixed in some
sections.
  -- color amino (and nucleic) acids of your choice.
  -- added support for more sequence file formats: MSF,
PAUP, PIR.  SeqApp now relies on the current Readseq code
for sequence reading & writing.
  -- save selection option to save subset of bases to file.
  -- addition the useful contig assembly program CAP,
written by Xiaoqiu Huang.
  -- major revision of preference saving method (less buggy,
I hope)
  -- major revision of the underlying application framework,
due to moving from MacApp 2 to MacApp 3.
  -- fixed a bug that caused loss of data when alignment
with a selection was saved to disk.

5 Oct 92, version 1.8a152+ -- a semi-major update with
various enhancements and corrections.  These include
- corrections to the main alignment display,
- improvements to the help system,
- major changes to the sequence print-out options,
-- including addition of a dotplot display (curtesy of
DottyPlot),
-- a phylogeny tree display (curtesy of TreeDraw Deck & J.
Felsenstein's DrawTree),
-- improved Pretty Print, which now has a single sequence
form and a better aligned sequence form,
-- improved Restriction map display,
- addition and updating of several e-mail service links,
-- including Blast Search and Genbank Fetch via NCBI,
-- BLOCKS, Genmark, and Pythia services,
- updated Internet gopher client (equal to GopherApp),
- editable Child Tasks dialogs
- addition of links to Phylip applications as Child Tasks
- addition of Phylip interleaved format as sequence output
option

11 June 92, version 1.6a35 is primarily a bug fix release.
Several of the  disasterous bugs have been squashed. This
version now works on the Mac SE model, except for sendmail.
No new features have been added.

7Jun92, v. 1.5a?? -- fixed several of the causes of
mysterious bombs  (mostly uninitialized handles), link b/n
multiseq and 1-seq views is better now, folded in GopherApp
updates, death date moved to Jan 93,

25Mar92, v1.5a32 (or later).  First release to general
public.  Includes Internet Gopher client.  Also released
subset as GopherApp for non-biologists.

4Mar92, v 1.4a38 -- added base sliding in align view. Bases
now slide something like beads on an abucus.  Select a
section with mouse, then grab section and shift left or
right. Gaps are inserted/removed as needed. For use as
contig aligner, still needs equivalent of GCG GelOverlap to
automatically find contig/fragment overlaps.

Also added "Degap" menu item, to remove "." and "-".  Fixed
several small bugs including Align pretty print which again
should display.

2Mar92, v 1.4a19 -- fixed several annoying bugs, see
SeqApp.Help, section on bugs for their resolution.  These
include Complement/Reverse/Dna2Rna/ Translation which should
work now in align view; Consensus menu item; entering
sequence in align window now doesn't freeze after 30+ bases;
pearson/fasta format reading; ...

10Feb92, v 1.4a6 -- fix for Mac System 6; add Internet
service dialogs for Univ. Houston gene-server, Geneid @ BU,
Grail @ ORNL; correct About Clustalv attribution.

5Feb92, v 1.4a4 -- limited release to network resource
managers, clustalv authors, testers.

Vers 1.4, Dec91 - Feb92. Dropped multi-sequence picker
window, made multi-align window  the primary view (no need
for both; extra confusion for users).  added pretty print,
restriction map, sequence conversions.   Generalized "call
clustal" to Hypercard-like, System 7 aware menu  for calling
external tasks. Fleshed out internet e-mail objects, added
help objects, window menu, nucleic/amino help windows. Many
major/minor revisions to all aspects to clean out bugs.
Preliminary release to a limited set of testers (1.4a?)

Vers. 1.3, Sept - Dec91. Modified clustalv for use as
external app (commandline file, background task, ...). Added
basic Internet e-mail routines call clustal routine
(preliminary child task)  Many major/minor revisions to all
aspects to clean out bugs.

Jun91-Aug91:  overwork at other tasks kept SeqApp on back
burner.

Mar91-Jun91: not much work on SeqApp, fleshed out TCP
methods (UTCP, USMTP, UPOP).

Feb 1991, vers 1.2? made available to Indiana University
biologists and NCBI biocomputists.

Vers. 1.1, Oct 1990, multiple sequence picker and multiple
sequence alignement window, including colored bases, added
to deal with alignment and common multi-sequence file
formats.

Version 1, Sep 1990. Single sequence edit window + TextEdit
window,  from MacApp skeleton/example source + readseq.