Downloading Genbank File Using Bioperl

Question

[meredith19]

Hi,

I am using Bio::DB::Eutilities to download genbank files. By default, the downloaded genbank files for sequences on the reverse strand are shown in the complement region. I was just wondering if there is any way to turn off the reverse complement option using BioPerl for these sequences. I am aware that there is a display option called "Show reverse complement" on the browser but I am looking for a BioPerl feature that turns off this option so that I can do it using a script.

Thanks

[Istvan Albert]

You need to distinguish between not having the data and not showing it. Even if the browser does not show the reverse strand the file still contains that information. In fact the file should always contain the reverse strand information otherwise it would not be a correct genbank file.

What does turn off the reverse complement mean? I suspect that your question is really about something else that you hope to achieve by modifying the genbank file. If so please edit the question (and title) to indicate that.

Do you mean something like: How to display every sequence as if it came from the forward strand?

Answer 1

[SES]

It sounds like you have used BioPerl to access e-utils and acquire a genbank file, and now you want to just select certain features from that file. If you are confident on the first part of this procedure and are wondering about the feature selection part, I would recommend reading the BioPerl Feature Annotation HOWTO page, which conveniently starts with a genbank file, and explains how to get certain features of interest. There are also more advanced topics on that page about doing things with coding sequences, obtaining annotations, etc. from a genbank file. Let us know if you have a more specific question in mind. Hope that helps.

[SES]

Hmmm, this appears to have been deleted (with no indication why) while I was writing my answer. I think it's a perfectly valid question.

[Istvan Albert]

it has been deleted while you wrote the answer - normally it can't be deleted after that