Software and DBs
Calculadora de Genes
A simulator of genetic crosses for mendelian traits, gene interactions and linkage. Creates Punnett Squares and histograms with phenotypic distributions of traits. Uses the distance to construct genetic two-, three- and four-point maps and, also, estimates genes distances given the progeny of a test cross for two- and three-point mpas (Gávez Salido & Navajas-Pérez, 2022).
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
[no longer available]
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
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
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).