Software and DBs

satDNA Analyzer

 

[Link]

A tool devoted to the classification of Strachan Transition States in samples of satellite DNA. It performs several computations, including nucleotide diversity and transitions/transversions. It shows results graphically in html format (Navajas-Pérez et al., 2007).

Plants Tandem Repeats Database

[Link]

A database of tandem repeats in eight plant genomes: the green alga Chlamydomonas reinhardtii, the moss Physcomitrella patens, the monocots rice and sorghum, and the dicots Arabidopsis thaliana, poplar, grapevine, and papaya (Navajas-Pérez & Paterson, 2009, Nagarajan et al., 2008).

Papaya Genomic Resources Online

[Link]

Papaya, Carica papaya L., has the first plant sex-determining region to be largely sequenced. This achievement together with the recent completion of the whole-genome sequence (WGS), will contribute to better understanding of papaya genome structure and organization. Papaya-DB stores, organizes and makes easily available papaya physical and genetic maps, shotgun WGS and EST sequences, and sex-determining region data to users, as well as providing an external link to the Plant Genome Duplication Database (PGDD) for whole-genome alignments with other plant species. We believe these resources will benefit the scientific community by contributing to answering important questions regarding plant-genome and sex-chromosome origin and evolution (Ming et al., 2008). Includes:

Papaya Repeat Database

[Link]

Papaya (Carica papaya L.) is an important fruit crop cultivated in tropical and subtropical regions worldwide. A first draft of its genome sequence has been recently released. Together with Arabidopsis, rice, poplar, grapevine and other genomes in the pipeline, it represents a good opportunity to gain insight into the organization of plant genomes. Here we report a detailed analysis of repetitive elements in the papaya genome, including transposable elements (TEs), tandemly-arrayed sequences, and high copy number genes. These repetitive sequences account for ~56% of the papaya genome with TEs being the most abundant at 52%, tandem repeats at 1.3% and high copy number genes at 3%. Most common types of TEs are represented in the papaya genome with retrotransposons being the dominant class, accounting for 40% of the genome. The most prevalent retrotransposons are Ty3-gypsy (27.8%) and Ty1-copia (5.5%). Among the tandem repeats, microsatellites are the most abundant in number, but represent only 0.19% of the genome. Minisatellites and satellites are less abundant, but represent 0.68% and 0.43% of the genome, respectively, due to greater repeat length. Despite an overall smaller gene repertoire in papaya than many other angiosperms, a significant fraction of genes (>2%) are present in large gene families with copy number greater than 20. This repeat database clarified a major part of the papaya genome organization and partly explained the lower gene repertoire in papaya than in Arabidopsis (Nagarajan et al., 2008).

Uso de cookies

Este sitio web utiliza cookies para que usted tenga la mejor experiencia de usuario. Si continúa navegando está dando su consentimiento para la aceptación de las mencionadas cookies y la aceptación de nuestra política de cookies

ACEPTAR
Aviso de cookies