The Journal of Heredity 2002:93(3)
© 2002 The American Genetic Association 93:225-227
FITMAPS and SHOWMAP: Two Programs for Graphical Comparison and Plotting of Genetic Maps
E. Graziano, and
P. Arúus
From the Institut de Recerca i Tecnologia Agroalimentàaries (IRTA); Departament de Genèetica Vegetal; Carretera de Cabrils s/n; 08348 Cabrils (Barcelona), Spain.
Address correspondence to Pere Arúus at the address above or e-mail: Pere.Arus{at}irta.es.
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Introduction
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Map comparisons are commonly used in genome analysis. Two maps
are typically constructed when using populations obtained from
a cross between two unrelated and partly heterozygous genotypes,
termed double pseudo-testcrosses or F
1 segregating progenies.
Each map contains all heterozygous markers of each parent, and
both maps can be connected with the markers that are heterozygous
in both parents (
Joobeur et al. 2000;
Maliepaard et al. 1998).
It is also common to compare maps generated with homologous
markers in different populations of the same species (
Danin-Poleg et al. 2000),
or for synteny studies among different species
(
Devos et al. 2000;
Grant et al. 2000). The number of markers
in each map is often significantly higher than the number of
shared markers, making handmade searches tedious and error prone.
Moreover, a graphical representation of the study would allow
fast appreciation of the relationships between the compared
maps. Here we announce the release of FITMAPS, a program for
fast comparison of maps, and its companion SHOWMAP, a program
for graphical plotting of single maps. Both programs generate
high-quality postscript files that can be customized through
many formatting options.
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System Requirements
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FITMAPS and SHOWMAP work on any Microsoft Windows computer with
Python installed. Python is a high-level interpreted language
freely available on the Internet at the Python website (
http://www.python.org).
If there is no postscript printer attached to the computer,
a postscript interpreter and viewer is required. The AFPL Ghostscript
interpreter is freely available at
http://www.cs.wisc.edu/~ghost/,
where the viewer GSview can be found as well. It is recommended
that you install Ghostscript and GSview, or similar programs,
even if a postscript printer is available, since this allows
you to preview the output pages and convert the output into
other graphic formats. The programs were developed and used
in a Microsoft Windows environment. They were tested on a Linux
system, showing no abnormal behavior. Since the source code
of both FITMAPS and SHOWMAP is available, it can be easily ported
to other systems, or changed to fit your special needs.
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Input Files
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The input files of both programs are plain text files. SHOWMAP
requires two input files: a data file and an options file. The
data file contains the map information. Its first line contains
the name of the map, and the following lines contain the names
and positions of each marker along the map, together with marker-specific
formatting options. SHOWMAP data files can be generated using
any text editor or by exporting Excel spreadsheet data. Alternatively,
MapMaker output data can be converted to the SHOWMAP data file
format by using a small utility program released with SHOWMAP
and FITMAPS, called MAKER2FIT. The options file stores all the
format options that are not specific of each marker, but general
to the whole map, such as the positioning of the map in the
output page and the scale at which it will be printed. The combination
of the settings stored in the data file and in the options file
gives a high degree of flexibility. Each marker can be highlighted
independently with bold, italic, or underline that can be used
in any combination, as well as 10 different colors. The map
can also be plotted with many drawing and formatting options,
including font scale, alignment of the markers, distance of
the marker names relative to the map line, and others. FITMAPS
uses two data files that follow the SHOWMAP data file format,
one for each of the maps that are compared, and one options
file. The compatibility between the two programs at the data
file level makes it possible that a map can be plotted alone
with SHOWMAP and compared to another map using FITMAPS. The
FITMAPS options file is similar to the SHOWMAP options file,
including all the settings available for SHOWMAP for each map,
plus new options to deal with the relationship between the two
maps, like the scaling between them, the color used to trace
the connecting lines, and the highlighting (or lack thereof)
that has to be applied to the markers that are shared between
both maps. The program can be launched from the DOS command
line, or the Linux shell by invoking the Python interpreter.
For users of Windows 95 or higher, a simple double-click on
the corresponding program file starts its execution.
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Output Files
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The output generated by both programs is postscript files (
Figure 1).
The number of formatting options available and the quality
of the output generated by postscript printers make them very
amenable for final publication. Moreover, with the aid of an
interpreter such as Ghostscript, the files can be easily converted
to PNG, TIFF, or BMP files, which can be used directly by standard
presentation or image processing software such as Microsoft
PowerPoint or Adobe Photoshop. Apart from the graphical output,
both programs store running information in a log file. The data
stored in the log file are especially useful when the program
stops running due to an incorrect format in any of the input
files. FITMAPS logs each correspondence that is found between
the two maps under comparison, saving the name of the shared
marker and its position in each map, yielding a convenient counterpart
to the graphical output.
View larger version (49K):
[in this window]
[in a new window]
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Figure 1.. Examples of FITMAPS output graphics. (A) Example of application of FITMAPS to fine map representation. Map data come from the almond map of Joobeur et al. (2000). (B) Use of FITMAPS for synteny studies with data from Prunus-Arabidopsis comparisons (Graziano E, Garriga-Calderée, and Arúus P, unpublished).
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Obtaining the Programs
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The programs can be downloaded from the IRTA website (
http://www.irta.es)
or requested by e-mail (
webmaster{at}irta.es). The programs are
packed in a zip file containing a user manual and some examples
of options files, data files, and generated output. Users with
no Internet access who have both Python and Ghostscript/GSview
can send a 1.44 Mb PC-formatted floppy disk to the corresponding
author, or a blank writable CD-ROM if these programs are not
available. Any further bug fixes and improvements will be provided
on the IRTA website.
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Acknowledgments
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This research was funded in part by European Union projects
BIO4-CT97-2170 and FAIR6-CT98-4139. E. Graziano is currently
at Unidad de Validacióon de Dianas, Almirall Prodesfarma.
Parc Cientíific de Barcelona, PBC4; Josep Samitier 1-5;
08028 Barcelona, Spain.
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Footnotes
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Corresponding Editor: Leif Andersson
Received March 21, 2001
Accepted January 30, 2002
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References
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Danin-Poleg Y, Teis N, Baudracco-Arnas S, Pitrat M, Staub JE, Oliver M, Aráus P, deVicente MC, and Katzir N, 2000. Simple sequence repeats in Cucumis mapping and map merging. Genome 43:963–974.[Medline]
Devos KM, Pittaway TS, Reynolds A, and Gale MD, 2000. Comparative mapping reveals a complex relationship between the pearl millet genome and those of foxtail millet and rice. Theor Appl Genet 100:190–198.[CrossRef]
Grant D, Cregan P, and Shoemaker RC, 2000. Genome organization in dicots: genome duplication in Arabidopsis and synteny between soybean and Arabidopsis. Proc Natl Acad Sci USA 97:4168–4173.[Abstract/Free Full Text]
Joobeur T, Periam N, deVicente MC, King G, and Arúus P, 2000. Development of a second generation linkage map for almond using RAPD and SSR markers. Genome 43:649–655.[Medline]
Maaliepaard C, Alston F, Van Arkel G, Brown LM, Chevreau E, Dunemann G, Evans KM, Gardiner S, Guilford P, van Heusden AW, Janse J, Laurens F, Lynn JR, Manganaris AG, den Nijs APM, Periam N, Rikkenrink E, Roche P, Ryder C, Sansavini S, Schmidt H, Tartarini S, Verhaegh JJ, Vrielink-van Ginkel M, and King G, 1998. Aligning male and female linkage maps of apple (Malus pumilla Mill.) using multi-allelic markers. Theor Appl Genet 97:60–73.
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Introduction
System Requirements