Message Boards Message Boards


Recommended import and navigation methods for whole genome of plant?

Posted 1 year ago
1 Reply
3 Total Likes

I'm interested in importing and navigating in Mathematica v12.2 desktop a recent GenBank whole genome of Ficus carica cultivar Dottato:

I've come up empty handed in the Wolfram Guides for BiomolecularSequences, ifeSciencesAndMedicineDataAndComputation, and SequenceAlignmentAndComparison.

Recommendations are welcome!

BTW, an interesting article about this sequence and assembly can be found here:

enter image description here

POSTED BY: Richard Frost

According to the web page, this has a GenBank ascension ID of CM019739.1. This can be used with a WFR function to import the sequence.

In[7]:= Short[
 genome = ResourceFunction["ImportFASTA"]["CM019739.1"], 10]

Out[7]//Short= {"CM019739.1 Ficus carica cultivar Dottato isolate GU2019 chromosome 1, whole genome shotgun sequence"},    

On a related note, an upcoming Wolfram blog (expected later this week) will cover usage of the Wolfram Function Repository functionality for genomic computation. It will of course have mention of ImportFASTA.

POSTED BY: Daniel Lichtblau
Reply to this discussion
Community posts can be styled and formatted using the Markdown syntax.
Reply Preview
or Discard

Group Abstract Group Abstract