Wolfram Function Repository

Instant-use add-on functions for the Wolfram Language

Function Repository Resource:

 ImportFASTA

Source Notebook

Import FASTA data from the NCBI using an NCBI Reference Sequence

Contributed by: Brendan Elli

ResourceFunction["ImportFASTA"][seqref]

imports FASTA data from the NCBI for the specified NCBI Reference Sequence seqref and returns its "Header" and "Sequence" elements combined into a list.

Examples

Basic Examples (2) 

Import a simple NCBI Reference Sequence and give the raw header and sequence:

In[1]:=
Short[mitoc = ResourceFunction["ImportFASTA"]["NC_013993"], 5]
Out[1]=

Use the chaos game representation to visualize this genome:

In[2]:=
srules = {"U" -> "T", Except[Characters["ACGT"]] -> ""};
In[3]:=
ResourceFunction["FCGRImage"][StringReplace[mitoc[[2, 1]], srules], 7]
Out[3]=

Publisher

Brendan Elli

Version History

  • 1.0.0 – 10 July 2019

Related Resources

License Information