Genbank File Format
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Entering edit mode
7 weeks ago
alenew.am • 0

Hi, can i ask you if there is a genbank file format in which the information of the row /product is merged with the row /locus tag? The reason is that in CLC it's useful to have the information about the gene product in the first /element, so that i can read the product name when i pass my pointer on the first element.

That is, from this (standard):

CDS             96..602
                     /locus_tag="SW30_001"
                     /codon_start=1
                     /transl_table=11
                     /product="HNH endonuclease"
                     /protein_id="AYP29987.1"
                     /translation="MPMVRRCKADGCRTLVERPAHYCTAHHSMEEERETYSRTRYNKR
                     VRNRDDETKERYAFYRSRTWSSIRKIALERDNYLCQYCLALGVTTPDARIGDHVTPVE
                     IAPELKTDVSNIVATCRSCDNTKRTLEQEIYGTGQNRTKQNTDLRLSVAAWAGLIARK
                     KADVVKPL"

To this (what i need):

  CDS             96..602
                     /locus_tag="SW30_001;HNH endonuclease"
                     /codon_start=1
                     /transl_table=11
                     /product="HNH endonuclease"
                     /protein_id="AYP29987.1"
                     /translation="MPMVRRCKADGCRTLVERPAHYCTAHHSMEEERETYSRTRYNKR
                     VRNRDDETKERYAFYRSRTWSSIRKIALERDNYLCQYCLALGVTTPDARIGDHVTPVE
                     IAPELKTDVSNIVATCRSCDNTKRTLEQEIYGTGQNRTKQNTDLRLSVAAWAGLIARK
                     KADVVKPL"

Thanks for your answer

gbkformat • 369 views
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Entering edit mode

Can you indicate if you need to do this within CLC or can use an external solution (if someone provides it here). If you need to do this inside CLC then consider contacting CLC tech support.

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Yes, it would be fine with an external solution, thanks for the reply

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I think this is a question for CLC support. It should be trivial for them to combine these fields into one. In other words, you need a better tool rather than a custom product on which that tool can work.

If you are not averse to Python programming, Biopython can read and write GenBank files. With a bit of code writing it should be easy to convert common GB files to the format you desire.

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Entering edit mode

Thanks, yes i have tried first here looking for a easier solution (for me), i didnt' know if this format was already available somewhere. thanks for the reply

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