Ncbi Standards For Genome Annotation After Contig Reduction

Question

[biotech]

Hi community,

I have been using a bacterial draft genome from GenBank for RNA-seq project. In order to reduce genome contig number, I used L_RNA_scaffolder enter link description here, so I had to reannotate again this new genome.

My doubt is how to publish now my RNA-seq results because I have the differential expressed genes with new annotations. I heard about the 'correspondence tables' but I really don't now how this work.

Thank you so much,

All the best, Bernardo

[Torst]

You will probably need to use BLASTP to find the orthologs in the original genome for each of the proteins in your new genome.

[biotech]

Thanks Torst, I will try to do this.

Answer 1

[biotech]

So, do you now how to get only the best BLASTp hit? Maybe:

blastp -db reference.faa -query DEG.faa -out DEG.xml -evalue 0.000001 -outfmt 5 -max_target_seqs 1