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using bioedit in capy certain gene in fasta formate in other new file

i have sequence resulting from assembly and I have certain gene names, I want to take these genes to other new file in fasta formate. Can anyone help me with the steps?, because i do the steps that i have known but do not working.

gene
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updated by venu venu • written by walaa.shaalan • walaa.shaalan

Can you provide more information such as sample files?

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written by Sej Modha Sej Modha

1 answer

If I understand correct, you would like to get the sequence of interested genes from your own assembly file.

If you do not have coordinates of the genes, it won't be possible to extract their sequences from the assembly file.

You might be interested to use a GTF file of your organism, if available (explained how to) in Ensemble or any other source. But this won't give accurate position of those genes in your assembly.

  • If your organism's GTF file is available, download it from Ensemble
  • Get the coordinates of your interested genes from downloaded GTF file in BED format.
  • Use bedtools getfasta to extract the sequences into a new file.
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written by venu venu

yes I have assembly file in fasta formate. and get the genes from KEGG and I want to select certain genes from the whole assembly that i have?

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written by walaa.shaalan • walaa.shaalan

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