Dot plot;
Genome assessment;
Interactive user interface;
Large genomes;
DOTPLOTS;
D O I:
10.7717/peerj.4958
中图分类号:
O [数理科学和化学];
P [天文学、地球科学];
Q [生物科学];
N [自然科学总论];
学科分类号:
07 ;
0710 ;
09 ;
摘要:
Dot plots are widely used to quickly compare sequence sets. They provide a synthetic similarity overview, highlighting repetitions, breaks and inversions. Different tools have been developed to easily generated genomic alignment dot plots, but they are often limited in the input sequence size. D-GENIES is a standalone and web application performing large genome alignments using minimap2 software package and generating interactive dot plots. It enables users to sort query sequences along the reference, zoom in the plot and download several image, alignment or sequence files. D-GENIES is an easy-to-install, open-source software package (GPL) developed in Python and JavaScript. The source code is available at https://github.com/genotoul-bioinfo/dgenies and it can be tested at http://dgenies.toulouse.inra.fr/.
机构:
Temple Univ, Inst Genom & Evolutionary Med, Philadelphia, PA 19122 USA
Temple Univ, Dept Biol, Philadelphia, PA 19122 USA
Temple Univ, Ctr Biodivers, Philadelphia, PA 19122 USATemple Univ, Inst Genom & Evolutionary Med, Philadelphia, PA 19122 USA
Kumar, Sudhir
;
Stecher, Glen
论文数: 0引用数: 0
h-index: 0
机构:
Temple Univ, Inst Genom & Evolutionary Med, Philadelphia, PA 19122 USA
Temple Univ, Dept Biol, Philadelphia, PA 19122 USATemple Univ, Inst Genom & Evolutionary Med, Philadelphia, PA 19122 USA
Stecher, Glen
;
Suleski, Michael
论文数: 0引用数: 0
h-index: 0
机构:
Temple Univ, Inst Genom & Evolutionary Med, Philadelphia, PA 19122 USA
Temple Univ, Ctr Biodivers, Philadelphia, PA 19122 USATemple Univ, Inst Genom & Evolutionary Med, Philadelphia, PA 19122 USA
Suleski, Michael
;
Hedges, S. Blair
论文数: 0引用数: 0
h-index: 0
机构:
Temple Univ, Inst Genom & Evolutionary Med, Philadelphia, PA 19122 USA
Temple Univ, Dept Biol, Philadelphia, PA 19122 USA
Temple Univ, Ctr Biodivers, Philadelphia, PA 19122 USATemple Univ, Inst Genom & Evolutionary Med, Philadelphia, PA 19122 USA
机构:
Temple Univ, Inst Genom & Evolutionary Med, Philadelphia, PA 19122 USA
Temple Univ, Dept Biol, Philadelphia, PA 19122 USA
Temple Univ, Ctr Biodivers, Philadelphia, PA 19122 USATemple Univ, Inst Genom & Evolutionary Med, Philadelphia, PA 19122 USA
Kumar, Sudhir
;
Stecher, Glen
论文数: 0引用数: 0
h-index: 0
机构:
Temple Univ, Inst Genom & Evolutionary Med, Philadelphia, PA 19122 USA
Temple Univ, Dept Biol, Philadelphia, PA 19122 USATemple Univ, Inst Genom & Evolutionary Med, Philadelphia, PA 19122 USA
Stecher, Glen
;
Suleski, Michael
论文数: 0引用数: 0
h-index: 0
机构:
Temple Univ, Inst Genom & Evolutionary Med, Philadelphia, PA 19122 USA
Temple Univ, Ctr Biodivers, Philadelphia, PA 19122 USATemple Univ, Inst Genom & Evolutionary Med, Philadelphia, PA 19122 USA
Suleski, Michael
;
Hedges, S. Blair
论文数: 0引用数: 0
h-index: 0
机构:
Temple Univ, Inst Genom & Evolutionary Med, Philadelphia, PA 19122 USA
Temple Univ, Dept Biol, Philadelphia, PA 19122 USA
Temple Univ, Ctr Biodivers, Philadelphia, PA 19122 USATemple Univ, Inst Genom & Evolutionary Med, Philadelphia, PA 19122 USA