Hi everyone,

I'm running BLASTP (all_vs_all) as part of my analysis. I merged all FASTA files from different species into a single file (merge.fast) and used it both as a query and as the database. The BLASTP execution itself went fine.

However, I noticed a discrepancy in gene naming for Arabidopsis thaliana between the protein FASTA file and the annotation GFF file—both downloaded from NCBI. A subset of each file is provided below for reference.

FASTA File Sample:

>NP_001030613.1 hypothetical protein 1 [Arabidopsis thaliana]
...
>NP_001030614.1 Phosphoglycerate mutase-like family protein [Arabidopsis thaliana]
...
>NP_001030615.2 ECA1-like gametogenesis related family protein [Arabidopsis thaliana]
...

GFF File Sample:

NC_003070.9	RefSeq	gene	3631	5899	.	+	.	ID=gene-AT1G01010;Dbxref=Araport:AT1G01010,TAIR:AT1G01010,GeneID:839580
NC_003070.9	RefSeq	mRNA	3631	5899	.	+	.	ID=rna-NM_099983.2;Parent=gene-AT1G01010;Dbxref=Araport:AT1G01010,GenBank:NM_099983.2
...

I also converted the GFF file into a 4-column format as required for MCScanX:

at003070.9	AT1G01010	3631	5899
at003070.9	AT1G01020	6788	9130
...

Issue:

When I ran MCScanX using:

./MCScanX ../synteny/ortho_mc/blast.tsv

I got the following result:

Reading BLAST file and pre-processing  
Generating BLAST list  
0 matches imported (0 discarded)  
0 pairwise comparisons  
0 alignments generated  
Pairwise collinear blocks written to /synteny/ortho_mc/.collinearity [0.000 seconds elapsed]  
Writing multiple syntenic blocks to HTML files  
Done! [0.000 seconds elapsed]  

It seems like no matches were imported.

Possible Cause & Question:

I suspect that the discrepancy in gene naming conventions between the protein FASTA file (NP_ accessions) and the GFF file (ATxGxxxxx locus IDs) might be the issue.

Does anyone know of a method, tool, or reference file to map NCBI protein accessions (NP_) to TAIR/Araport gene locus IDs (ATxGxxxxx)?
Or is there a better way to resolve this issue for MCScanX?

Any help or pointers would be greatly appreciated!

Thanks in advance!