Globodera pallida Synteny with H.glycines

Downloadable File
Organism: 
Heterodera glycines v2 (Soybean Cyst Nematode (v2))
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: 
04/06/2018
Materials & Methods (Description and/or Program Settings): 
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
Category: