Bacterial gene annotation

Question

[biotech]

We are not being able to perform protein expression of four cloned genes. Since the cause could be that genes are not well annotated and thus unstable at protein level, I would like to know how to reannotae these genes and compare old vs new annotation.

Genome was annotated using NCBI PGAAP annotation pipeline.

Thanks

Answer 1

[dago]

This is kind of strange question. If you want to "annotate" some prtoein sequences there are plenty of tools out there.

Starting from more general search using Blastp, to more restricted search for domains using TIGRFAM, Pfam or using the combination of tools offered by INTERPRO.

Since you do not provide detail on the old annotation procedure I would say it is quite impossible outline a good procedure to compare the outcome of the annotations

[biotech]

Thanks sago. What I'm trying to say is that its possible that these genes have an alternative ORF, maybe longer. What I was thinking is to reannotate the genomic region again using other annotation pipeline and then compare old vs new annotation. Here is a Biostars post with some tools: Bacterial Annotation Pipeline

[dago]

I would say that you can use one of the tools mentioned in the link you provide and compare the results with your actual annotation. Sorry, but I miss the question here.