How to do blastp for MCScanx if i have genomic protein and gff?
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7 weeks ago
bioinfo223 ▴ 10

Hello,

I'm new to bioinformatics and I have a question about using MCScanX for a particular species. I have the genomic protein sequences and a GFF file for this species. However, after running BLASTP, I noticed that the IDs in the BLASTP results correspond to protein IDs, while the IDs in the GFF file represent gene IDs. As a result, when I use MCScanX, I'm getting zero synteny. Can you please advise me on how to resolve this issue? Thank you.

diamond blastp -e 1e-5 -p 30 -q v1_protein.faa -d GCF.aa -a augustus.aa.vs.self  -b8 -c1

x.blast

NP_0013471.1  NP_0013471.1  100     166     0       0       1       166     1       166     2.30e-116       327
NP_0013471.1  XP_0425915.1  78.3    166     32      1       1       166     1       162     1.51e-86        252

x.gff

chr1    gene-LOC1226577       8679    12187
chr1    gene-LOC1226575       2966    7093
chr1    gene-LOC1092258       25095   34175
chr1    gene-LOC1090128       35304   50351
synteny MCScanx • 152 views
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