After alignment imported GBK file lost the mutation portion and stripped the gap.

K M Taufiqur Rahman

• November 17, 2020 23:21

Hello, 

After pairwise alignment (MAFFT, MUSCLE is not working) I transferred the annotation to other sequence. But whenever I tried to import this sequence in gene bank file then all the mutations and gap stripped. Thus, the base pair also reduced and lost sequence overall integrity. But if I keep this file in geneious format then its alright. So my query is how can I make GB file keeping all things as it is. 

Thanks a lot for your assistance.

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  Hilary Miller

  • November 18, 2020 00:25

  Please send us a copy of your file via the Contact Us button in Geneious so that we can see what the formatting looks like.  Note that Genbank format is not an alignment format, so it will just export the individual sequences in the alignment and not the gaps introduced during the alignment.  You would be better to export in fasta format if you want a file containing aligned sequences. 

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  K M Taufiqur Rahman

  • November 20, 2020 22:48

  Thank you for the information. Okay I will send the file. Could you please assist to resolve another problem that I am not able to import my contig file  which is 5GB in size but small size file easily imported. Thanks

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  Hilary Miller

  • November 23, 2020 00:57

  Its best if you can contact us directly with details of your computer specs and the file you are trying to import. 

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