Genome Annotation Submission Syntax Check

Question

[zhliu.tju]

Dear all,

I proposed to use some submission syntax check software in order to evaluate the quality of some automated annotation services' results, such as RAST and IMG. I have used sequin, however I have found that although it can point out some mistakes in the annotations. For example, brackets are not allowed in the annotations. But I still can find some annotation which are unsuitable for annotation submission. For instance, some of them contain EC ID in the annotations.

I have checked the NCBI tool and did not find anything seems to meet this end. I do not know if the EMBL/KEGG provide these kind of annotation syntax or format check services?

Thanks a lot and I am looking forwards your reply!

Zhe

Answer 1

[Torst]

You can check bacterial genome submissions online at NCBI here: http://www.ncbi.nlm.nih.gov/genomes/frameshifts/frameshifts.cgi

And there is also a stand-alone command line version called SUBCHECK: ftp://ftp.ncbi.nih.gov/genomes/TOOLS/subcheck

[zhliu.tju]

Thanks a lot, Torst. I have a look at both of the tools and it seems that these two tools make the gene recognition and annotation check. I am not quite sure that it will make the syntax check or not. For instance, it will check if certain words are not allowed or suitable in the annotation, like plural form of protein "proteins" and other criteria such as shown here http://www.ncbi.nlm.nih.gov/genbank/genomesubmit_annotation. Anyway, thanks a lot for your reply and I found it is useful.