Missing pseudogenes in annotation report

Hi all,

I used spades for assembly of bacteria-Illumina reads, and galaxy-Prokka for annotation Visualization of the annotation results showed me:

Summary of the active entries: contigs: 65

bases: 5736331

CDS: 5102

gene: 5279

misc_RNA: 52

rRNA: 9

tRNA: 115

tmRNA: 1

1- how can I confirm that annotation results are correct? 2- I am confused, why there are no pseudogenes in my report!!

Thanks for your time

assembly

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written 6.1 years ago by Pegasus •

As far as I know, PROKKA does not give you pseudogenes in the genome. You should manually focus on pseudogenes, such as C, N-terminus missing fragmented on ORF. However, I do not know If there is another method to find pseudogenes in the genome.

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written 6.1 years ago by young_bioinformatician

Thanks ugurcabuk for the answer. I wonder if it's essential to find pseudogenes in order to publish a draft genome, and submit it into NCBI !!

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written 6.1 years ago by Pegasus •

Hi Seraph, I think, you can send an e-mail to NCBI submission portal (http://genomes@ncbi.nlm.nih.gov) about it. By the way, I found something that can be useful. See the link.

PGAP

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written 6.1 years ago by young_bioinformatician

Hi ugurcabuk

I tried to use this tool, but as I am a beginner, I am still facing this problem; NCBI PGAP yami file

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written 6.1 years ago by Pegasus •

please, make sure the file is executable. If not, you can do it using chmod +x. Or you can call it through python pgap.py.
some descriptions about yaml file is on the tool's github page, wiki section. See the link. Input-files

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written 6.1 years ago by young_bioinformatician

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