I want to download exon-wise gene sequence of around 200 genes from NCBI. Is there anyway to do this from terminal? I have the transcript id for each sequence and I am using efetch command to download their CDS.

eg: efetch -db nuccore -format fasta_cds_na -id NM_000125.4

However, I need their exon-wise sequence as well (i.e. I need the sequence of each exon separately). It will be better if the exon starts with start codon and ends with stop codon (the untranslated regions of those exons completely removed) but I can modify the sequences accordingly once I have all the sequences (UTR included).

Is there any way in which we can give the NCBI transcript id as an input and get exon-wise sequence as an output?



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