Program, Pipeline Name or Method Name

Opscan ortholog calling, iadhore syntenic fragment

Program, Pipeline or Method version

Opscan 0.1, iAdHoRe 3.0.01

Source Name

H. glycines synteny with G. rostochiensis genome (2016)

Time Executed

April 5, 2018, midnight

Category

Genome structure

Description

Genome from this publication: Eves-van den Akker S, Laetsch DR, Thorpe P, Lilley CJ, Danchin EG, Da Rocha M, Rancurel C, Holroyd NE, Cotton JA, Szitenberg A (2016) The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence. Genome biology 17:124 Fastp and global alignments with Opscan (0.1) (Drillon et al. 2014). All alternatively spliced variants and all possible multi-family genes were considered. To infer synteny, iAdHoRe 3.0.01 (Proost et al. 2011) was used with prob_cutoff=0.001, level 2 multiplicons only, gap_size=15, cluster_gap=20, q_value=0.9, and a minimum of 3 anchor points. Drillon G, Carbone A, Fischer G (2014) SynChro: a fast and easy tool to reconstruct and visualize synteny blocks along eukaryotic chromosomes. PloS one 9:e92621 Proost S, Fostier J, De Witte D, Dhoedt B, Demeester P, Van de Peer Y, Vandepoele K (2011) i-ADHoRe 3.0—fast and sensitive detection of genomic homology in extremely large data sets. Nucleic acids research 40:e11-e11

File

rostochiensis_syntenic_ribbons_txt_gfffixed_sorted.gff_.gz

Index

rostochiensis_syntenic_ribbons_txt_gfffixed_sorted.gff_.gz.tbi