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. pallida genome (2017)

Time Executed

April 6, 2018, midnight

Category

Genome structure

Description

Genome from this publication:Cotton JA, Lilley CJ, Jones LM, Kikuchi T, Reid AJ, Thorpe P, Tsai IJ, Beasley H, Blok V, Cock PJ (2014) The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode. Genome biology 15:R43. 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

pallida_syntenic_ribbons_sorted_txt_gff_sorted.gff_.gz

Index

pallida_syntenic_ribbons_sorted_txt_gff_sorted.gff_.gz.tbi