Computational protocol: Comparative physical genome mapping of malaria vectors Anopheles sinensis and Anopheles gambiae

Similar protocols

Protocol publication

[…] OrthoDB was used to identify one-to-one orthologues from An. sinensis and An. gambiae and to determine their locations on the scaffolds []. The comparative positions of the orthologous genes from An. sinensis and An. gambiae were plotted using genoPlotR []. Synteny blocks for each pair of homologous chromosome arms between An. sinensis and An. gambiae were analysed from the database generated by OrthoDB (Additional file ). Chromosomal regions containing two or more orthologous genes with the same order and orientations were defined as synteny blocks and numbered 1, 2, 3, etc. along the chromosomes. After obtaining the number of all synteny blocks, the inversion distances on homologous chromosome arms between An. sinensis and An. gambiae were estimated using the programs of Genome Rearrangements in Mouse and Man (GRIMM) []. […]

Pipeline specifications

Software tools genoPlotR, GRIMM
Databases OrthoDB
Application Genome data visualization
Diseases Malaria