O'Reilly logo

Bioinformatics with R Cookbook by Paurush Praveen Sinha

Stay ahead with the world's most comprehensive technology and business learning platform.

With Safari, you learn the way you learn best. Get unlimited access to videos, live online training, learning paths, books, tutorials, and more.

Start Free Trial

No credit card required

Retrieving a sequence

To start the task of sequence analysis, the first thing we need is a sequence of DNA or protein. Such sequence data can be retrieved either by visiting the database hosting page via a browser or by accessing the data mart form within R via corresponding commands/functions. We had a look at some of the methods in the previous chapter. In this recipe, we introduce some more methods to retrieve a sequence.

Getting ready

Retrieving sequences from databases requires the following:

  • Access to the database via the Internet
  • A sequence ID or keyword for searching
  • The biomaRt and seqinr libraries installed and loaded in the R session

How to do it…

To fetch a sequence of the data via R, perform the following steps:

  1. Get a sequence of the data. ...

With Safari, you learn the way you learn best. Get unlimited access to videos, live online training, learning paths, books, interactive tutorials, and more.

Start Free Trial

No credit card required