How to do Genome Annotation?
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5.5 years ago

Dear sir/mam,

In need help regarding Genome Annotation. I have Streptococcus Pneumonia .Fastq data, i have done mapping using bowtie 2 tool and aligned data i converted from .bam file to .fasta format. Know how to do Genome annotation using GeneDB or other tools.

Need help

Thank you

GenomeAnnotation • 1.6k views
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5.5 years ago

You can download the genome assembly and annotation in different format from NCBI: https://www.ncbi.nlm.nih.gov/genome/176 Unless you have a completely novel strain, you should not attempt to annotate yourself.

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Hi Thanks for the suggestions

i need help from this paper http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0169370 where they have done Genome annotation using GB, MLST analysis i have query how to get fasta sequence data from mapping alignment .bam file

after converting to.fa file the file looks like this is this the correct one.

Screen shot of .fasta file after converting

Need help

Thank you

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Sorry, I do not understand your request.

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5.5 years ago
Joe 20k

Use prokka by Torsten Seeman:

http://www.vicbioinformatics.com/software.prokka.shtml

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5.5 years ago
Denise CS ★ 5.2k

How about Maker? Have you checked if the genome is not already annotated in Ensembl Bacteria? They've got several strains of Streptococcus pneumoniae in there.

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14 months ago
sagnik ▴ 50

Hello,

We have developed a gene annotator called FINDER which can annotate eukaryotic genomes using short-read RNA-Seq reads and protein sequences. It is completely automated and requires no manual intervention. FINDER also runs BRAKER to incorporate predicted genes in the repertoire. You can access the paper from FINDER and the software from here GitHub.

Thank you.

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