Journal of Heredity Advance Access originally published online on August 31, 2005
Journal of Heredity 2005 96(5):623-625; doi:10.1093/jhered/esi099
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Computer Note |
Atlas: A Java-Based Tool for Managing Genotypes
From BSD Devices – AGB, Paseo del Rey 10, 28008 Madrid, Spain (E. Pérez-Enciso and García-Bernal); Institut Catalá de Reçerca i Estudis Avançats, Pg Lluis Companys 23, 08010 Barcelona, Spain (M. Pérez-Enciso); and Departament de Ciència Animal i del Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain (M. Pérez-Enciso)
Address correspondence to Miguel Pérez-Enciso, Departament de Ciència Animal i del Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain, or e-mail: miguel.perez{at}uab.es.
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Abstract |
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With the exponential increase in genotyping capability, it is fundamental to check data consistency and improve genotype management. Atlas is a Java-based application for managing genotypes that also provides a series of tools useful in traceability, parentage testing, and identification, as well as pedigree and marker visualization.
Despite the increasing genotyping capability and that molecular markers are being used in an expanding number of fields, ranging from quantitative trait loci studies (Lynch and Walsh 1998) to traceability (Meghen et al. 1998) to paternity testing (Avise 1994), there is almost no public software that facilitates its management and includes tools useful for these tasks. The GEMMA database (Iannuccelli et al. 1996) includes some useful capabilities, but it is not publicly available. While paternity testing is implemented in, for example, CERVUS (Slate et al. 2000), or pedigrees can be viewed with Pedigree Viewer (http://www-personal.une.edu.au/
bkinghor), although without marker information, Atlas provides a single platform to carry out all these tasks. Atlas provides a standalone, easy to use, and easy to install Java application for managing genotypes. Atlas can be particularly useful in some specialized instances, such as parentage testing and traceability. Many breeder's associations require that the animal be paternity tested before being accepted to a herdbook. Atlas provides a tool to check genotype consistency between parents and offspring, underlining the incompatible genotypes. Furthermore, in some instances, the exact parent is not known, but the potential sires (or dams) are available; Atlas provides an automated utility to determine the compatible parents among a set of potential parents. Although this can be done by hand, it is time consuming and prone to error. In parallel, traceability is becoming an important public issue (McKean 2001). Atlas facilitates the traceability of biological samples by determining how many different genotypes there are between any pair of selected samples. The pairs can then be ranked according to the number of mismatches. Finally, a visual appraisal of the pedigree and genotypes facilitates interpretation of the results. Atlas allows us to draw the genotypes of an individual and its closest relatives (parents, mates, and offspring), and is able to draw any number of markers simultaneously. It also allows for sex-specific markers, that is, it permits a single allele per marker in males.
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Program Description |
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Atlas requires the Java 2 Runtime Environment (JRE) SE version 1.4 be installed on your equipment (http://java.sun.com/j2se/1.4.2/download.html).
Atlas is able to deal with any number of files (tables) simultaneously, although operations are carried out only in the selected file. A typical Atlas file contains the following fields: individual, father, mother, sex, markers, and auxiliary. Only the individual field is strictly obligatory. The user can change the names of the marker and auxiliary columns; the rest of column names (individual, father, mother, sex) are protected. Auxiliary fields can be used to hold, for example, performances recorded, disease status, age, etc. Atlas files are protected and each user has access only to his or her own files, unless they are unprotected.
There exists an import utility that facilitates incorporating ASCII files into Atlas format. The tool is quite flexible and allows the user to determine the column positions corresponding to each field, the sex code, or the first and last rows to be imported. If the information is contained in several files (e.g., pedigree and genotypes in different files), the Atlas merging utility can be used to combine different tables. On importing or merging, possible duplicates in the individual code are tested, as well as incompatibilities between genotypes. Atlas does not reconstruct phases via, for example, coalescence techniques (Li and Stephens 2003), but does determine, based on pedigree information, whether an allele is of paternal, maternal, or undetermined origin. Alleles of known paternal (maternal) origin are shown in blue (red).
Currently there are six main menus in Atlas. These are File (tools for opening, closing, exporting, importing, merging, and printing files), Edit (tools for deleting and inserting individuals and fields), Database (protects and unprotects files, depending on the user), Tools (for checking incompatibilities, proposing parents, and drawing pedigrees), Windows (for selecting of the active file), and Help.
The three main tools available in Atlas are # genotype differences, parent compatibility, parent proposal, and pedigree drawing. The option # genotype differences returns the number of allele differences between an individual and a subset (or all) of the remaining individuals. This option is useful for traceability purposes. Samples that pertain to the same individual must show no genotype differences, although a minimum number of mismatches can be due to genotyping errors.
Marker compatibility between parents and offspring can be checked for all individuals or for a selected subset. A list of incompatible genotypes is written in a new table and incompatible genotypes are underlined in the original table.
It is also possible to determine compatible parents from a set of potential parents selected by the user or from all available individuals. This option is applicable only if at least one parent is missing. The user can click on an individual among the compatible parents panel and set it as father or mother. The program distinguishes between males and females (e.g., if an individual with mother known is tested, only males are candidates). Consequently the user is not allowed to set a female as father or a male as mother.
The pedigree drawing tool draws schematically the marker information of an individual and its parents, mates, and offspring (see Figure 1). Alleles can be shown in black (by default) or color, according to parent origin (by clicking on the icon on the top left of the window).
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This program is free for noncommercial applications and is available at http://www.icrea.es/pag.asp?id=Miguel.Perez. Contact Miguel Pérez-Enciso (miguel.perez{at}uab.es) otherwise, as a fee will be required. The downloadable .zip file contains a Read Me file with all required instructions, the executable program, a manual, and a small example file. The Java 2 Runtime Environment (JRE) SE version 1.4 must be installed on your equipment (http://java.sun.com/j2se/1.4.2/download.html).
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Acknowledgments |
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This work was funded by Ministerio de Educación y Ciencia grants AGL2004-00103/GAN and AGL2004-08378-C02 (Spain). We are grateful to Armand Sánchez for encouragement and N. Jiménez, A. Tomás, A. Molina, O. Ruiz, F. Rendo, and A. Estonba for testing the program and comments.
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Footnotes |
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Corresponding Editor: Leif Andersson
Received January 25, 2005
Accepted June 23, 2005
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Avise JC, 1994. Molecular markers, natural history and evolution. New York: Chapman & Hall.
Iannuccelli N, Woloszyn N, Arhainx J, Gellin J, and Milan D, 1996. GEMMA: a database to manage and automate microsatellite genotyping. In: Proceedings 25th International Conference on Animal Genetics, Tours, France, July 21-26, 1996. Anim Genet 27(suppl 2):88.
Li N and Stephens M. 2003. Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics 165:2213–2233.
Lynch M and Walsh B, 1998. Genetics and analysis of quantitative traits. Sunderland, MA: Sinauer Associates.
McKean JD, 2001. The importance of traceability for public health and consumer protection. Rev Sci Tech Off Int Epiz 20:363–371.
Meghen CM, Scott CS, Bradley DG, Machug DE, Loftus RT, and Cunningham EP, 1998. DNA based traceability techniques for the meat industry. Anim Genet 29:48–59.[CrossRef][Medline]
Slate J, Marshall T, and Pemberton J, 2000. A retrospective assessment of the accuracy of the paternity inference program CERVUS. Mol Ecol 9:801–808.[CrossRef][Medline]
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