download genbank sequences with exon sequences highlighted

Question

[kspata]

Hi,

I wish to download genbank sequence for KRAS with all the exonic regions highlighted. GenBank has an option of 'Highlight Sequence Feature' which displays exons one at a time. But I want to highlight these sequences (exons only) in the downloaded GenBank file.

https://www.ncbi.nlm.nih.gov/nuccore/NG_007524.1?&feature=any#feature_NG_007524.1_exon_0

Is there a way to do this with NCBI while downloading the sequence? Or I have to do it manually which will take time and is more prone to errors.

Thanks in advance.

[Sej Modha]

If you are after coding sequences then following would work:

esearch -db nuccore -query NG_007524.1|efetch -format fasta_cds_na

However, like genomax2 mentioned in the comment, it is not possible to 'highlight sequences'.

[GenoMax]

Sequence is normally in text format so any annotation (like the highlighting that you refer to) is applied on top/after the fact.

You may be able to use UCSC Table browser which offers an option of downloading genomic sequences with Exons in upper case, everything else in lower case. That may fit your need of being able to distinguish the exons from the rest of the sequence.

[kspata]

Hi genomax,

Thank you for replying. Your suggestion is the most close to what I need. Also, on Ensemble you can download the sequence with exons highlighted in the RTF (Rich Text Format).

https://useast.ensembl.org/Homo_sapiens/Gene/Sequence?g=ENSG00000133703;r=12:25204789-25250936

However, as you and Sej mentioned there is no other way to highlight a sequence in Genbank format.

Thank you for your help!!!

Answer 1

[Dattatray Mongad]

You can use efetch from ncbi-entrez-direct utilities. But first, you must have the accessions (with start and end of seuences which you want to extract). Make one file for this data and use following command in any script.

efetch -db nuccore -id NG_007524.1 -format fasta -chr_start start -chr_stop stop

[GenoMax]

I know you want to help but please check the requirements in original question before you provide answers.

But I want to highlight these sequences (exons only) in the downloaded GenBank file.

Your solution does not satisfy that requirement. It only retrieves the sequence.