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 M. hapla genome (2008)

Time Executed

April 6, 2018, midnight

Category

Genome structure

Description

Genome from this publication: Opperman CH, Bird DM, Williamson VM, Rokhsar DS, Burke M, Cohn J, Cromer J, Diener S, Gajan J, Graham S, Houfek TD, Liu Q, Mitros T, Schaff J, Schaffer R, Scholl E, Sosinski BR, Thomas VP, Windham E (2008) Sequence and genetic map of Meloidogyne hapla: A compact nematode genome for plant parasitism. Proceedings of the National Academy of Sciences 105:14802-14807. 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

hapla_syntenic_ribbons_txt_gff_sorted.gff_.gz

Index

hapla_syntenic_ribbons_txt_gff_sorted.gff_.gz.tbi