Mummer

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2.5 years ago

saifulislam99121 • 0

Hello, I am using mummer. I am facing a problem using mapview command. This command needs e .cds file and .utr file in GFF format. How can I get that? I have assemble file in FASTA format and prokka annotation file.

The command is mapview [options] <coords file> [UTR coords] [CDS coords]

Mummer • 887 views

ADD COMMENT • link updated 2.5 years ago by iraun 6.2k • written 2.5 years ago by saifulislam99121 • 0

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Hi! Please, edit your title so that is a bit more informative of the issue you are specifically having with mummer tool. Having said this, and without knowing exactly the species you are working on, you can download annotation and CDS files in Ensembl. For the CDS you go to the fasta subfolder and for the anotation to gtf or gff3 subfolders.

ADD REPLY • link 2.5 years ago by iraun 6.2k

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Sorry for late replly. I am working with Acinetobacter lwoffii, Acinetobacter towneri. How can I get the CDS and gff file?

ADD REPLY • link 2.5 years ago by saifulislam99121 • 0

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Are you there??

ADD REPLY • link 2.5 years ago by saifulislam99121 • 0

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Hi! Sorry, I rarely work with bacteria. Doing a quick google search, I found this GFF3 file. If you have the genome, using the gff3 you can extract the CDS sequences and UTR.

ADD REPLY • link 2.5 years ago by iraun 6.2k

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