PubMed Health⌕ Search
Home/Archive/PubMed

PubMed · 15374870

MAP-O-MAT: internet-based linkage mapping.

X Kong·T C Matise
View original source ↗Export metadata ↓

Abstract

UNLABELLED: MAP-O-MAT is a web-based server for automated linkage mapping of human polymorphic DNA markers. MAP-O-MAT facilitates the verification of order and map distances for custom mapping sets using genotype data from the CEPH database, and from the Marshfield, SNP Consortium and Rutgers linkage maps (exclusive to the deCODE genotyping data). The CRI-MAP program is used for likelihood calculations and some mapping algorithms, and physical map positions are provided from the human genome assembly. AVAILABILITY: MAP-O-MAT is located at http://compgen.rutgers.edu/mapomat/ CONTACT: matise@biology.rutgers.edu.

Explore related subjects

Chromosome MappingGenetic MarkersInternetSequence AlignmentSequence Analysis, DNASoftwareUser-Computer InterfaceJournal ArticleResearch Support, N.I.H., ExtramuralResearch Support, Non-U.S. Gov'tResearch Support, U.S. Gov't, P.H.S.

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

X Kong, T C Matise. 2004-09-16. MAP-O-MAT: internet-based linkage mapping.. https://doi.org/10.1093/bioinformatics%2Fbti024

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2026

Mitotic karyotyping and FISH mapping of the gender-specific locus indicate an advanced XY system in Hippophae rhamnoides.

Hippophae rhamnoides ssp. turkestanica, a subdioecious plant inhabiting the cold desert of the Indian Himalaya, has gained immense recognition for its nutritional and medicinal values. In recent years, the plant species has proven to be a suitable system to understand the evolution of dioecy. Despite its biological significance, the cytogenetics of this dioecious plant is unclear due to various conflicting accounts of its X-Y chromosome system, particularly the length of Y-chromosome. In this study, we resolved these ambiguities through comprehensive cytogenetic analyses across diverse western Himalayan populations. Using morphometric analysis and fluorescence in situ hybridization (FISH) with a gender-specific marker (HRMSSR), we confirmed homomorphic XX chromosomes in females and heteromorphic sex-chromosomes in males with a notably smaller Y-chromosome. The investigation also revealed a predominant somatic chromosome number of 2n = 24, although minor deviations (2n = 18, 20, 22) appeared at the seed level. These findings highlight an evolutionarily advanced sex-chromosome system. This first detailed cytogenetic investigation of Himalayan Seabuckthorn provides critical insights into the chromosomal architecture, laying a crucial foundation for future evolutionary, genomic, and conservation studies in the species.

Chromosome Mapping↗
PubMed2007

Methods for linkage disequilibrium mapping in crops.

Linkage disequilibrium (LD) mapping in plants detects and locates quantitative trait loci (QTL) by the strength of the correlation between a trait and a marker. It offers greater precision in QTL location than family-based linkage analysis and should therefore lead to more efficient marker-assisted selection, facilitate gene discovery and help to meet the challenge of connecting sequence diversity with heritable phenotypic differences. Unlike family-based linkage analysis, LD mapping does not require family or pedigree information and can be applied to a range of experimental and non-experimental populations. However, care must be taken during analysis to control for the increased rate of false positive results arising from population structure and variety interrelationships. In this review, we discuss how suitable the recently developed alternative methods of LD mapping are for crops.

Chromosome Mapping↗
PubMed2007

An efficient method for producing an indexed, insertional-mutant library in rice.

Generation of an indexed, saturated, insertional-mutant library is an aid to understanding the functions of genes in an organism. However, 10 years of work by many investigators have not yet yielded such a library in rice. The major reason is that determining the chromosomal locations of a very large number of random insertion mutants by flanking sequence analysis is highly labor intensive, and therefore, libraries that do exist have not been indexed. We report here an efficient procedure to construct an indexed, region-specific, insertional-mutant library of rice. The procedure makes use of efficient long-PCR-based high-throughput indexing, coupled with a random but anchored population of Ds transposants. Long-PCR indexing allows rapid and simultaneous determination of the chromosomal locations of a large number of mutants that surround a particular anchor line, thus converting a random library into an indexed one. Such a library can be used directly, without the need to screen a large random library for a desired mutant plant.

Chromosome Mapping↗