Question: fasta + gff -> genbank
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gravatar for j.dolata
2.5 years ago by
j.dolata0
j.dolata0 wrote:

Hi I would like to extract data in genbank format based on genome fasta file and gff file with coordinates. Could anybody help me?

genbank sequence gff fasta genome • 1.4k views
ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by j.dolata0

Yes, I have fasta file with whole genome and using gff file I would like to obtain genbank file. I have already tried with EMBOSS Seqret but I have obtained genbank file containing one LOCUS (corresponding to whole chromosome) and list of features (from gff file) below, and at the end sequence of whole chormosome... so this is not what I need.

ADD REPLYlink written 2.5 years ago by j.dolata0

That is how a GenBank file is formatted. Sounds like you don't want a standard GenBank file.

Please use ADD REPLY/ADD COMMENT when responding to existing posts to keep threads logically organized.

ADD REPLYlink written 2.5 years ago by genomax65k
0
gravatar for genomax
2.5 years ago by
genomax65k
United States
genomax65k wrote:

Let me make sure this is what you want. You have a fasta file and the GFF annotation and you want to build a GenBank format file combining the two? Sorry to nitpick but since GenBank is a more complex format you are not extracting information here but synthesizing it from simpler pieces.

It also helps to search biostars before posting new questions: Converting Gff/Gtf + Reference To Embl Or Genbank ...Any Tools Available?

Edit: I am not sure why @Wouter asked you to post this as a new question unless the inference I am drawing above is incorrect.

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by genomax65k

genbank format should looks:

LOCUS gene1 FEATURES (for gene1) gene mRNA CDS ORIGIN (sequence of gene 1) // LOCUS gene2 FEATURES (for gene2) gene mRNA CDS ORIGIN (sequence of gene 2) //

Using Seqret I've got:

LOCUS chromosome1 FEATURES (for all genes in gff file) ORIGIN (sequence of chromosome1)

ADD REPLYlink written 2.5 years ago by j.dolata0
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