Using BioPerl to retrieving multiple sequences from a genome

Question

[ggman]

Fellow Biostars

I have a question about what I am doing. Keep in mind I am not asking for a script it is more of a conceptual question as I have downloaded bioperl just now and am attempting to use it. I am providing the steps I am taking and asking whether or not I am able to accomplish this through using BioPerl.

From the table, Table 1: Sequence Object Methods, from the Bioperl page, I can see that using $string = $seq_obj->subseq(x,y) can retrieve a sequence based on one set location running from x to y. This could be modified to retrieve multiple sequences if I place the coordinate locations that are assigned to a name in a separate file.

Such as say the file looks like

name1 15 20
name2 35 50

I'll have those values be transferred to x and y accordingly and looped through so I get the corresponding sequences from the genome and the name that accompanies the particular sequence.

I can accomplish this through using Bioperl's $string = $seq_obj->subseq(x,y) if I code everything else accordingly correct?

[ggman]

Hello ggman!

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It's been answered.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

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Cheers!

Answer 1

[Ram]

Yes.

<<Achievement Unlocked: Answer a question with one word.>>

[ggman]

Cool! Thank you for taking the time to read this.

[Ram]

To mark the question solved, moderate-> close is not the right way. Instead, accept the answer(s) that you find best address your question. The system will mark the question answered and stylize the post differently on the home page.

[ggman]

sorry i was not aware of that..