Cabot, E., L.;Beckenbach, A., T.
doi: 10.1093/bioinformatics/5.3.233pmid: 2766009
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Orozco,, Modesto;Luque, F., J.
doi: 10.1093/bioinformatics/5.3.241pmid: 2766013
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doi: 10.1093/bioinformatics/5.3.199pmid: 2766006
Abstract This paper presents a FORTRAN IV subroutine to calculate inbreeding and kinship coefficients from pedigree information in a diploid population without self-fertilization. The user can specify the number of ancestral generations to be taken into account. It is thus possible to determine contributions of succeeding ancestral generations to the inbreeding and kinship coefficients under consideration. The subroutine is based on a recursive procedure that generates systematically all paths connecting two individuals, NP and NM, whose kinship coefficient is to be calculated (or between the father NP and the mother NM of the individual whose inbreeding coefficient is to be calculated). These paths obey the following conditions: (i) a given path does not contain the same parent—offspring link more than once; (ii) the vertex of a path is an ancestor common to individuals NP and NM, with a rank lower or equal to the parameter specified in input. Constraints regarding the size of the corpus of genealogical data and the storage method are discussed, as well as the interest of this subroutine compared to the existing ones. An example of application is given. This content is only available as a PDF. © IRL Press Limited
doi: 10.1093/bioinformatics/5.3.183pmid: 2766005
Abstract An algorithm for correspondence analysis is described and implemented in SAS/IML (SAS Institute, 1985a). The technique is shown, through the analysis of several biological examples, to supplement the log-linear models approach to the analysis of contingency tables, both in the model identification and model interpretation stages of analysis. A simple two-way contingency table of tumor data is analyzed using correspondence analysis. This example emphasises the relationships between the parameters of the log-linear model for the table and the graphical correspondence analysis results. The technqiue is also applied to a three-way table of survey data concerning ulcer patients to demonstrate applications of simple correspondence analysis to higher dimensional tables with fixed margins. Finally, the diets and foraging behaviors of birds of the Hubbard Brook Forest are each analyzed and then a simultaneous display of the two separate but related tables is constructed to highlight relationships between the tables. This content is only available as a PDF. © IRL Press Limited
Le,, Shu-Yun;Owens,, John;Nussinov,, Ruth;Chen,, Jih-H.;Shapiro,, Bruce;Maizel, Jacob, V.
doi: 10.1093/bioinformatics/5.3.205pmid: 2475224
Abstract A method for assessing the preserved stem - loops of RNA secondary structures is presented. Frequently recurring helical stems in a set of secondary structures resulting from the simulated folding process of a given RNA are assessed and consensus structural motifs can then be selected to construct a secondary structure of the RNA. Alternatively, it can be applied to a series of ‘optimal’ and ‘suboptimal’ secondary structures computed using the dynamic program developed by Williams and Tinoco. To demonstrate the power and the usefulness of the program we give examples of this procedure. This content is only available as a PDF. © IRL Press Limited
Cockwell, Kerri, Y.;Giles, Ian, G.
doi: 10.1093/bioinformatics/5.3.227pmid: 2766008
Abstract Two programs, MOTIF and PATTERN, that scan sequences for matches to user-defined motifs and patterns of motifs based on identity and set membership are described. The programs use a simple and logical notation to define motifs, and may be used either interactively or by using command line parameters (suitable for batch processing). The two programs described also incorporate a simple, yet reliable, algorithm that automatically detects in which of six possible formats the sequence entry is written. This content is only available as a PDF. © IRL Press Limited
doi: 10.1093/bioinformatics/5.3.247pmid: N/A
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Liu,, Jingdong;Parkinson, John, S.
doi: 10.1093/bioinformatics/5.3.237pmid: 2766011
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Marszalek,, J.;Kostrowicki,, J.;Spychala,, J.
doi: 10.1093/bioinformatics/5.3.239pmid: 2766012
Article PDF first page preview Close This content is only available as a PDF. Author notes *Present address: Division of Biophysics, Department of Molecular Biology, University of Gdansk, ul. Kladki 24, 80-822 Gdansk, Poland © IRL Press Limited
doi: 10.1093/bioinformatics/5.3.248pmid: N/A
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