Hello Everyone,

I am trying to do a synteny analysis using MCScanX. As per requirement I have done all by all blast between two sets of protein from two closely related species. And also prepared the gff file. The file formats are as follows:

cyp_dan.blast

NP_001347641.1 NP_001347641.1 100.00 166 0 0 1 166 1 166 3e-120 341 NP_001347641.1 XP_042591522.1 78.31 166 32 1 1 166 1 162 5e-91 267 NP_001347641.1 XP_042577882.1 60.24 166 62 2 1 166 1 162 4e-63 196 . . XP_704272.2 XP_018953536.1 31.03 87 59 1 275 360 90 176 8e-07 50.4 XP_704272.2 NP_001005958.2 33.33 63 38 1 273 331 38 100 1e-06 48.9 XP_704272.2 XP_018969808.1 31.33 83 56 1 275 356 91 173 2e-06 49.3

cyp_dan.gff

NC_056572.1 gene-LOC1221465.1 2966 7093 NC_056572.1 id-LOC122146575.1 2966 3166 NC_056572.1 id-LOC122146575.1 3246 3357 . . NC_002333.2 gene-CYTB;Dbxre.1 15308 16448 NC_002333.2 cds-NP_059343.1.1 15308 16448 NC_002333.2 gene-trnT;Dbxre.1 16449 16520

cmdline: /home/software/MCScanX/MCScanX cyp_dan

But i am getting the collinearity output like as:

MATCH_SCORE: 50

MATCH_SIZE: 5

GAP_PENALTY: -1

OVERLAP_WINDOW: 5

E_VALUE: 1e-05

MAX GAPS: 25

Number of collinear genes: 0, Percentage: 0.00

Number of all genes: 108556

Here, both of the species are from same family since there is no chance to have "zero collinear gene".

In this circumstances I hope, i will get your suggestions that can aid me to solve my analysis. Thanks.