Hasil untuk "Maps"

Wenqi Ren, Sibo Liu, Hua Zhang et al.

Paul B. Garrett

L. Meng, Huihui Li, Luyan Zhang et al.

Abstract QTL IciMapping is freely available public software capable of building high-density linkage maps and mapping quantitative trait loci (QTL) in biparental populations. Eight functionalities are integrated in this software package: (1) BIN: binning of redundant markers; (2) MAP: construction of linkage maps in biparental populations; (3) CMP: consensus map construction from multiple linkage maps sharing common markers; (4) SDL: mapping of segregation distortion loci; (5) BIP: mapping of additive, dominant, and digenic epistasis genes; (6) MET: QTL-by-environment interaction analysis; (7) CSL: mapping of additive and digenic epistasis genes with chromosome segment substitution lines; and (8) NAM: QTL mapping in NAM populations. Input files can be arranged in plain text, MS Excel 2003, or MS Excel 2007 formats. Output files have the same prefix name as the input but with different extensions. As examples, there are two output files in BIN, one for summarizing the identified bin groups and deleted markers in each bin, and the other for using the MAP functionality. Eight output files are generated by MAP, including summary of the completed linkage maps, Mendelian ratio test of individual markers, estimates of recombination frequencies, LOD scores, and genetic distances, and the input files for using the BIP, SDL, and MET functionalities. More than 30 output files are generated by BIP, including results at all scanning positions, identified QTL, permutation tests, and detection powers for up to six mapping methods. Three supplementary tools have also been developed to display completed genetic linkage maps, to estimate recombination frequency between two loci, and to perform analysis of variance for multi-environmental trials.

M. Kanehisa, M. Araki, S. Goto et al.

KEGG (http://www.genome.jp/kegg/) is a database of biological systems that integrates genomic, chemical and systemic functional information. KEGG provides a reference knowledge base for linking genomes to life through the process of PATHWAY mapping, which is to map, for example, a genomic or transcriptomic content of genes to KEGG reference pathways to infer systemic behaviors of the cell or the organism. In addition, KEGG provides a reference knowledge base for linking genomes to the environment, such as for the analysis of drug-target relationships, through the process of BRITE mapping. KEGG BRITE is an ontology database representing functional hierarchies of various biological objects, including molecules, cells, organisms, diseases and drugs, as well as relationships among them. KEGG PATHWAY is now supplemented with a new global map of metabolic pathways, which is essentially a combined map of about 120 existing pathway maps. In addition, smaller pathway modules are defined and stored in KEGG MODULE that also contains other functional units and complexes. The KEGG resource is being expanded to suit the needs for practical applications. KEGG DRUG contains all approved drugs in the US and Japan, and KEGG DISEASE is a new database linking disease genes, pathways, drugs and diagnostic markers.

G. Klein, D. Murray

P. Wessel, Walter H. F. Smith

D. Olson, E. Dinerstein, E. Wikramanayake et al.

Jonathan Harel, C. Koch, P. Perona

W. Bosma, John J. Cannon, Catherine Playoust

John Ashburner John

John M. Lee

John G. K. Williams, A. Kubelik, Kenneth J. Livak et al.

S. Wiggins

R. Hadsell, S. Chopra, Yann LeCun

T. Kohonen

P. Wessel, Walter H. F. Smith

Walter H. F. Smith, D. Sandwell

L. Itti, C. Koch

W. T. Tutte

Maulidya Maghfiro, Ni Wayan Surya Wardhani, Atiek Iriany

The purpose of this study is to evaluate and compare different clustering techniques, including hierarchical cluster analysis (using complete linkage, average linkage, and single linkage methods), Self-Organizing Maps (SOM) clustering, and ensemble clustering, within the framework of integrated cluster analysis combined with Naïve Bayes analysis, specifically applied to cabbage production in Indonesia. The data utilized in this study are on cabbage production from various districts and cities in Indonesia, obtained from the 2023 publications of the Central Statistics Agency (BPS). The variables used in this study are cabbage harvest, cabbage production, area height, and rainfall. The data size used is 157 districts/cities in Indonesia. This research is a quantitative analysis employing integrated cluster analysis combined with Naïve Bayes. Cluster analysis is used to obtain classes in each district/city. Different clustering methods, including hierarchical clustering, Self-Organizing Map (SOM), and ensemble clustering, are compared to determine the best approach for grouping districts based on cabbage production. Naïve Bayes analysis is then used to classify cabbage production in Indonesia and identify the optimal clusters. This comparison aims to find the most effective clustering method for improving grouping accuracy and understanding cabbage production patterns. The best method for classifying cabbage production in Indonesia is the ensemble clustering approach integrated with Naïve Bayes, resulting in three distinct clusters: high, medium, and low production clusters.