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
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.
Use prokka by Torsten Seeman:
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.
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.
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
version 2.3.6
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
Sorry, I do not understand your request.