PubMed Health⌕ Search
Home/Archive/PubMed

PubMed · 10592192

INE: a rice genome database with an integrated map view.

K Sakata·B A Antonio·Y Mukai·H Nagasaki·Y Sakai·K Makino·T Sasaki
View original source ↗Export metadata ↓

Abstract

The Rice Genome Research Program (RGP) launched a large-scale rice genome sequencing in 1998 aimed at decoding all genetic information in rice. A new genome database called INE (INtegrated rice genome Explorer) has been developed in order to integrate all the genomic information that has been accumulated so far and to correlate these data with the genome sequence. A web interface based on Java applet provides a rapid viewing capability in the database. The first operational version of the database has been completed which includes a genetic map, a physical map using YAC (Yeast Artificial Chromosome) clones and PAC (P1-derived Artificial Chromosome) contigs. These maps are displayed graphically so that the positional relationships among the mapped markers on each chromosome can be easily resolved. INE incorporates the sequences and annotations of the PAC contig. A site on low quality information ensures that all submitted sequence data comply with the standard for accuracy. As a repository of rice genome sequence, INE will also serve as a common database of all sequence data obtained by collaborating members of the International Rice Genome Sequencing Project (IRGSP). The database can be accessed at http://www. dna.affrc.go.jp:82/giot/INE. html or its mirror site at http://www.staff.or.jp/giot/INE.html

Explore related subjects

Chromosomes, Artificial, YeastDatabases, FactualGenome, PlantOryzaUser-Computer InterfaceJournal ArticleResearch Support, Non-U.S. Gov't

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

K Sakata, B A Antonio, Y Mukai, H Nagasaki, Y Sakai, K Makino, T Sasaki. 2000-01-01. INE: a rice genome database with an integrated map view.. https://doi.org/10.1093/nar%2F28.1.97

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

KEEP EXPLORING

Related citations

PubMed2006

Markers, selection, and media in yeast artificial chromosome cloning.

Yeast have proven to be a valuable and flexible host for cloning and manipulating large fragments of foreign genetic material, providing valuable reagents for the study of gene function and regulation in a variety of applications. However, this approach requires a familiarity with basic procedures derived from yeast genetics, and lack of experience can be a barrier to researchers with backgrounds limited to bacterial and mammalian culture systems. To address this issue, this chapter introduces and discusses the genetic markers and selection systems used in the genetic manipulation of yeast, with particular reference to yeast artificial chromosome (YAC) cloning and manipulation. Detailed descriptions of culture media are provided, allowing for the growth and selection of standard YAC strains, as well as for specialist applications.

Chromosomes, Artificial, Yeast↗
PubMed2006

A polymerase chain reaction-mediated yeast artificial chromosome-splitting technology for generating targeted yeast artificial chromosomes subclones.

The yeast artificial chromosomes (YAC) system makes it possible not only to clone large DNA fragments but also to simplify the physical mapping and functional analysis of chromosomes and genomes through YAC manipulation. To manipulate large DNA fragments cloned into YACs, YAC fragmentation has been developed and also a new method called the YAC-splitting method was developed recently. Although the YAC fragmentation method can be used to delete DNA from one side of a YAC, the YAC-splitting method generates two smaller YACs, both of which are transmitted to daughter cells during mitotic growth. This chapter describes the YAC-splitting method improved by incorporating polymerase chain reaction-mediated chromosome splitting (PCS) technique and by adding yeast autonomously replicating sequence (ARS) to the system. The PCS method combines a streamlined procedure (two-step PCR and one transformation per splitting event) with the Cre/loxP system for marker rescue. The improved YAC-splitting method can convert a targeted region of a eukaryotic chromosome within a YAC into a new replicating YAC.

Chromosomes, Artificial, Yeast↗
PubMed2006

Genomic reconstruction by serial mitotic recombination of yeast artificial chromosomes.

DNA cloned in yeast artificial chromosomes (YACs) is a valuable resource for functional experiments in cell culture as well as whole animal systems. Where the size or chimerism of a YAC clone are limiting factors it may be desirable to generate recombinant YAC clones. One such approach is based on mitotic recombination, and we describe the development of a methodology that allows multiple recombination cycles for serial reconstruction of overlapping YACs. This approach employs retrofitting with standard plasmid vectors, transfer of YACs to a common haploid host by Kar1 mating, and selection for recombination with 5-fluoro-orotic acid.

Chromosomes, Artificial, Yeast↗