NAME
boxshade - Pretty-printing of multiple sequence alignments
SYNOPSIS
boxshade
DESCRIPTION
BOXSHADE is a program for pretty-printing multiple alignment output.
The program itself doesn´t do any alignment, you have to use a multiple
alignment program like ClustalW or Pileup and use the output of these
programs as input for BOXSHADE.
This manual page was written for the Debian(TM) distribution because
the original program does not have a manual page. The presented
information comes from the documentation of the Web Service of the 3.21
version that is not available as a Debian package.
BOXSHADE is a program for creating good looking printouts from
multiple-aligned protein or DNA sequences. The program does no
alignment by itself, it has to take as input a file preprocessed by a
multiple alignment program or a multiple file editor. See below for a
list of supported input formats and output devices. In the standard
BOXSHADE output, identical and similar residues in the
multiple-alignment chart are represented by different colors or
shadings. There are some more options concerning the kind of shading to
be applied, sequence numbering, consensus output and so on. The user
interface is a bit clumsy at the moment, one has to answer a lot of
questions in order to get the desired output. There is, however, the
possibility to use default parameters from a standard parameter file or
to supply the program with parameters from the command line. At the
moment, the VMS and DOS versions of BOXSHADE have identical user
interfaces.
Input formats
BOXSHADE 3.2 knows about the following input file formats: (some of the
are generally used only for MSDOS or VMS systems) + CLUSTAL and
CLUSTALV, multiple alignment program, DOS/VMS/MAC default extension
.ALN + ESEE, multiple sequence editor, DOS default extension .ESE +
PHYLIP, phylogenetic analysis package, DOS, VMS, UNIX default extension
.PHY + PILEUP and PRETTY of the GCG sequence analysis package VMS/UNIX
default extensions .MSF and .PRE NB!! you are strongly encouraged NOT
to use the PRETTY format as input, it may be incompatible with the
revised version of .MSF input. We can´t actually think why anyone would
use this format now, .MSF files are more useful generally. + MALIGNED,
multiple sequence editor, VMS only default extension .MAL BOXSHADE
tries to determine the file type from the extension but will work also
if different extensions are used.
Output devices
POSTSCRIPT/EPS creates POSTSCRIPT(TM) files for printing on a
Laserprinter or for further conversion with a POSTCRIPT interpreter
(like GHOSTSCRIPT) + HPGL for export to various graphics programs or
for conversion/printing with the shareware program PRINTGL. Plotting
BOXSHADE output on a plotter is generally not recommended + RTF for
export to various word-processing and graphics programs + CRT, uses
direct screen writes to the PC-monitor. Possible options depend on the
graphics adapter used. This output device is supported only in the
MSDOS version. + ANSI. On a PC, this option uses an ANSI device driver
(ANSI.SYS) that has to be loaded in CONFIG.SYS previously. Possible
character renditions are reverse, bold,underlined, blinking etc. On
non-DOS systems, this option behaves more or less like the VT100 output
mode. + VT100 for display on a VT100 compatible terminal or emulator. +
ReGISterm for display on a ReGIS compatible graphics terminal or
emulator. + ReGISfile for later conversion by the program RETOS
(copyright DEC) in order to print on DIGITALs printer series. + LJ250
for printing on DIGITALS LJ250 color printer. + ASCII output showing
either the conserved residues or the varying ones (others as ´-´). +
FIG file for xfig 2.1. + PICT files for import to Mac and PC graphics
progs. Some of the formats above offer the possibility of scaling the
characters and of rotating the plot. Character size has to be entered
in ´point´ units. Normal output orientation is in portrait mode
(PS/EPS/HPGL/PICT only), to obtain output in landscape orientation,
´rotate plot = y´ has to be chosen. When creating multi-page output,
all pages are contained in a single output file. If one page per file
is desired, one has to use the command line parameter /SPLIT. This is
enforced when requesting EPSF or PICT file output, as multi-page EPSFs
are a contradiction of the purpose of an EPSF and large PICT files
would probably be too big for most personal computers. While using the
terminal as output device, the ´RETURN´ key has to be pressed to obtain
the next page of output.
Sequence numbering
Starting with version 2.2 there is the possibility to add numbering to
the output files. The numbers are printed between the sequence names
and the sequence itself. Since most of the input-files either use no
numbering or number the first position in the alignment always with a
"1" (and that does not necessarily reflect the numbers within the
original sequence), the user is asked to enter the starting position
for each sequence. The command line flag /DEFNUM suppressed that
question, a starting position of 1 is assumed for all sequences.
Boxshade starts with the value entered for the leftmost position and
continues numbering every valid symbol, skipping blanks, ´-´,´.´ and
stuff like that.
Default parameters
Several people using previous releases of BOXSHADE pointed me to the
need of having default parameters for the various questions asked by
the program. They argued that most sites only use one type of input
files, one output device and one choice of colors for the output. I
therefore added a management of default parameters allowing two levels
of assistance to the user. 1) all default parameters are contained in
an ASCII file that can be modified easily to accomodate the users
taste. The format is roughly documented within the file-header, it
resembles the keyboard input one has to make if using the program
interactively. There are two such files supplied with this release of
BOXSHADE, BOX_DNA.PAR and BOX_PEP.PAR , holding some example parameters
for peptide and dna-comparisons. there are no big differences between
these two, the major one is that when shading DNA-comparisons one
doesn´t care of "similar" residues. 2) to run the program with minimal
user interaction, I have added the possibility to use command line
parameters. At the moment, you can use: /check : list all allowed
command line paramters (this list) and allows parameters to be added.
/def : program runs without questions, BOX_PEP.PAR is used as default
/dna : makes the program use BOX_DNA.PAR as parameter file /pep : makes
the program use BOX_PEP.PAR as parameter file /in=xxx : makes the
program take xxx as input file /out=yyy : makes the program take yyy as
output file (note1) /par=zzz : makes the program use zzz as a default
parameter file /type=1 : makes the program assume an input file of type
1 (PRETTY/MSF) /dev=1 : makes the program assume and output device of
type 1 (CRT) /numdef : use default numbering (all sequences starting
with "1") /thr : threshold fraction of residues that must agree for a
consensus /split : forces one page per file output, creates multiple
output files. /cons : makes the program create an additional consensus
line (see below) /symbcons=: influences the way the consensus line is
displayed. (see below) /unix : writes output files in unix style (LF
only) (note2) /dos : writes output files in DOS style (CR/LF) (note2)
note1: on unix machines, use out=OUTPUT for terminal output on DOS
machines, use out=con: on VMS machines, use out=tt: note2: if no mode
is specified, the native style of the machine is used.
ATTENTION
on unix systems, the dash (-) instead of the slash (/) has to be used
as separation character for command line paramters. For example, a
valid unix command line is: boxshade -def -numdef -cons -symbcons=" .*"
Shading strategies (similarity to consensus or single sequence)
Starting with version 3, BOXSHADE has a new shading system. The first
difference is the introduction of a threshold fraction of residues that
must agree for there to be a consensus. Previously, the program assumed
that SOME residue was always the consensus. If no two residues were the
same, the first sequence provided the consensus residue. This threshold
fraction can be any number between 0.0 and 1.0. The number of sequences
that must agree for there to be a consensus is, as you might expect,
this fraction times the total number of sequences in the alignment
(fractions of a sequence count as one, e.g. 3.2 becomes 4). The second
difference is the idea of ´consensus by similarity´; this tries to take
account of the situations where all the sequences may have (for
example) R or K at a position, but neither in a majority. It would not
be logical to shade one type of residue as ´identical´ and the other as
´similar´; the threshold function might also eliminate both as being in
too small numbers. Therefore, if there is not a single residue that is
conserved (greater than the threshold) at a position, the program looks
for a ´group´ of amino acids that fulfills the requirements. ´Groups´
are defined in the .grp files. Users can tailor these to their personal
prejudices. Any amino acid not listed is assumed not to be in a group.
All members of a group are considered to be mutually similar, unlike
the .sim files, described below. If consensus by similarity is found,
all the residues in the consensus are shaded using the ´similar´
shading defined by the user. If the user does not select ´shading by
similarity´, only identity-type consensus is looked at. If an
identity-type consensus is found, and similarity shading is in
operation, the program looks to see if the remaining residues are
similar to the consensus residue. Here the box_xxx.sim files are used.
The main difference between relationships in these files and those in
the .grp files is that, e.g. in a .grp file the line STA means that all
three a.a.s are mutually similar. In a .sim file S TA means that both T
and A are considered similar to S, where there is a conserved S residue
in more than threshold number of sequences. However, it does NOT mean
that T and A are similar to each other. Note that cases where two
residues, or groups of residues, fulfill the threshold requirements (as
could happen with values of the thr. fraction less than or equal to
0.5) are treated as having no consensus. This describes the main
shading model ´shading according to a consensus´. The alternative model
is called ´shading according to a master sequence´. In this case the
user is prompted for a sequence of the alignment and consecutively that
sequence is taken to be the ´consensus´. Only those residues become
shaded that are identical or similar to the chosen sequence. Output
obtained with this option tends to be less shaded and neglects
similarities beween the other (non-chosen) sequences. Starting in V2.7,
this ´master sequence´ can be hidden. Thus, it only influences the
shading of the other sequences without being shown itself.
Consensus display
Starting with version 2.5, BOXSHADE offers the possibility to create an
additional line holding a consensus symbol. This line can either be
obtained by using the command line qualifier /CONS or interactively by
answering the question ´ create consensus? ´. The way this consensus
line is displayed can be modified by the command line parameter
SYMBCONS=xyz, by editing the respecitve entry in the .PAR file or
interactively. Since the SYMBCONS syntax is not intuitive, here a brief
description: The SYMBCONS parameter consist of exactly three symbols: +
the first one stands for ´normal´ sequence residues that are not
involved in any similar/identical relationship. + the second symbol
represents positions that are similar in all sequences of the
alignment. See the files BOX_PEP.SIM and BOX_DNA.SIM to see what
residues are considered similar. + the third symbol represents
positions that are identical in all sequences of the alignment. A
SYMBCONS parameter string " .*" (blank/point/asterisc) means: label all
positions in the alignment with totally identical residues by an
asterisc, all positions with all similar residues by a point and do not
mark the other positions. The letter ´B´ can be used instead of the
blank, this is necessary e.g. when using the command line option
/SYMBCONS=B.* which gives the same result as the above example. The
option /SYMBCONS= .* would result in an unexpected behaviour because
MSDOS squeezes blanks out of the command line. Besides points,
asteriscs and other symbols, there are two special characters when they
appear in the SYMBCONS string: ´L´ and ´U´. An ´L´ means, that a
lowercase representation of the most abundant residue at that position
is to be used instead of a fixed consensus symbol while an ´U´ means an
uppercase character representation of that residue. A possible
application would be the SYMBCONS string " LU" where similar residues
are represented by lowercase characters and identical by uppercase
characters.
Shareware/PD programs useful in conjunction with BOXSHADE
multiple alignment files that to be used by BOXSHADE can be created,
amongst others, by the following PD/freeware programs: + PHYLIP by Joe
Felsenstein, available by ftp from anthro.utah.edu + ESEE by Eric
Cabot, available from the same sources as BOXSHADE (see above) +
CLUSTAL by Des Higgins, ditto for preview/conversion of POSTSCRIPT
files, the program GHOSTSCRIPT from GNU software foundation is highly
recommended. It is available from all major MSDOS ftp-sites (e.g.
SIMTEL or ftp.uni-koeln.de) There is also a version tested for use with
boxshade available at vax0.biomed.uni-koeln.de although this might be
not the most recent release. for Mac users, there is MacGhostscript,
also available from the main archives (info-mac, umich and their
mirrors). A *very* good tool for putting a preview image into an EPSF
file, often a prerequisite for incorporating into a drawing package, is
PS2EPS, by Peter Lerup. This can be found on info-mac. for
preview/conversion of HPGL files, the shareware program PRINTGL 1.18 by
Cary Ravitz is highly recommended. It is available from many MSDOS ftp
sites and from netserv@embl-heidelberg.de - output on dot printers -
Since PRINTGL offers a broad choice of printer types and is a nice
program, I recommend its use for printing BOXSHADE output on
non-POSTSCRIPT printers. Use HPGL output with options 0F1N for normal
residues 2F1N for identical residues 3F1N for similar residues 2F4N for
conserved residues 8 for character size not rotated (these are the
standard parameters in BOX_PEP.PAR) for creating a HPGL files. (lets
call it TEST.PLT) Now use PRINTGL either interactively by calling PMI
or use a command line like: PRINTGL /Fx/S0340/Waaac/Ptest.plt where
test.plt is to be replaced by the filename to convert and the x in the
expression /Fx is to be replaced by the letter of the printer you use.
(See the PRINTGL documentation for further details)
RESTRICTIONS
The RTF output and PHYLIP input implementations are still experimental.
Please tell me of your experiences with the program. + the current DOS
version supports only 13 sequences with 2000 residues each. This
parameters can be easily changed in the source code. If you cannot
compile the sources because you are lacking a pascal compiler, contact
the author for precompiled versions
CITING BOXSHADE
There is no publication on BOXSHADE and none is planned. Most people
just use it for figures in publications and don´t mention anything,
this is ok for the authors of BOXSHADE. If you really feel like
mentioning BOXSHADE, you could either acknowledge it in the figure
legend or in the Mat&Meth part on sequence analysis.
SEE ALSO
/etc/boxshade/*.par
seaview(1) kalign(1)
AUTHORS
Kay Hofmann <kay.hofmann@memorec.com>
ISREC, Bioinformatics Group,
CH-1066
Epalinges s/Lausanne Switzerland
Wrote Boxshade.
Michael Baron <michael.baron@bbsrc.ac.uk>
BBSRC Institute for Animal Health,
Pirbright,
Surrey
GU24 0NF
U.K.
Wrote Boxshade.
Harmut Schirmer <hsc@techfak.uni-kiel.de>
Technische Fakultaet,
Kaiserstr. 2
D-24143
Kiel
Germany
C port of Boxshade. (don´t send Kay or Michael any questions
concerning the ´C´ version of boxshade)
Steffen Möller <steffen_moeller@gmx.de>
Wrote the manpage.
Charles Plessy <charles-debian-nospam@plessy.org>
Updated the manpage
COPYRIGHT
Copyright © 1997 Kay Hofmann, Michael Baron and Harmut Schirmer
Copyright © 2003, 2007 Steffen Moeller, Charles Plessy
The above copyright notices refer to the program and its manpage
respectively.
BOXSHADE is completely public-domain and may be passed around and
modified without any notice to the authors.
This manual page was written for the Debian(TM) system but may be used
by others. Permission is granted to copy, distribute and/or modify this
document under same terms as boxshade itself.