Program, Pipeline Name or Method Name

Braker,Opscan ortholog calling, iadhore syntenic fragment

Program, Pipeline or Method version

braker1.9, Opscan 0.1, iAdHoRe 3.0.01

Source Name

H. glycines synteny with G. ellingtonae genome (2017)

Time Executed

April 6, 2018, midnight

Category

Genome structure

Description

Genome from this publication: Phillips WS, Howe DK, Brown AM, Eves-Van Den Akker S, Dettwyler L, Peetz AB, Denver DR, Zasada IA (2017) The Draft Genome of Globodera ellingtonae. Journal of nematology 49:127. 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

ellingtonae_syntenic_ribbons_txt_gff_sorted.gff_.gz

Index

ellingtonae_syntenic_ribbons_txt_gff_sorted.gff_.gz.tbi