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 EnsemblGenomeAssemblyConversion

Source Notebook

Convert chromosome coordinates on one genome assembly to another

Contributed by: Keiko Hirayama

ResourceFunction["EnsemblGenomeAssemblyConversion"][assembly1, assembly2,{chromosome,start,end}]

converts chromosome coordinates specified by the start and end positions on the genome assembly1 to assembly2.

Details and Options

EnsemblGenomeAssemblyConversion is based on Ensembl, which provides comparative genomics information.
Genome assembly is the complete DNA sequence of an organism reconstructed from the smaller segments of sequenced nucleotides.
EnsemblGenomeAssemblyConversion can be used to convert the genome positions from the archived assemblies to those of more recent assemblies, or vice versa.
Inputs to the EnsemblGenomeAssemblyConversion include the common names of the input and output genome assemblies, as well as the chromosome positions in the input assembly, specified by the chromosome name and integer-based start and end coordinates.
Chromosome names are given by integer numbers or short names such as "1", "X", "mt" for chromosome 1, X, mitochondrion, respectively.
The following option can be given:
"Species""human"species for which to query; following scientific names and common names of species are accepted: "Homo sapiens", "human", "Mus musculus", "mouse", "Danio rerio", "zebrafish", "Caenorhabditis elegans", "Saccharomyces cerevisiae"

Examples

Basic Examples (2) 

Convert the human chromosome coordinates on the previous genome assembly, GRCh37, to the latest assembly, GRCh38:

In[1]:=
ResourceFunction[ "EnsemblGenomeAssemblyConversion", ResourceSystemBase -> "https://www.wolframcloud.com/obj/resourcesystem/api/1.0"]["GRCh37", "GRCh38", {"X", 1000000, 1000100}]
Out[1]=

Convert the zebrafish chromosome coordinates on the latest genome assembly, GRCz11, to the previous assembly, GRCz10:

In[2]:=
ResourceFunction[ "EnsemblGenomeAssemblyConversion", ResourceSystemBase -> "https://www.wolframcloud.com/obj/resourcesystem/api/1.0"]["GRCz11", "GRCz10", {10, 30000, 30100}, "Species" -> "Danio rerio"]
Out[2]=

Scope (5) 

Use the EnsemblPhenotype function to find the genomic variation location associated with dysosteosclerosis:

In[3]:=
genomefeature = ResourceFunction["EnsemblPhenotype"]["dysosteosclerosis", "GenomicFeatures"]
Out[3]=

Use the EnsemblGenomeAssemblyConversion to convert the variation associated chromosomal coordinates on the latest genome assembly to the previous one:

In[4]:=
precoord = ResourceFunction[ "EnsemblGenomeAssemblyConversion", ResourceSystemBase -> "https://www.wolframcloud.com/obj/resourcesystem/api/1.0"]["GRCh38", "GRCh37", ToExpression@StringSplit[genomefeature[1, "Location"], ":" | "-"]]
Out[4]=

Retrieve the DNA sequence associated with the identified genomic variation. Use NCBIEntrezData function to get the nucleotide accession for human chromosome 10:

In[5]:=
chr10acc = ResourceFunction["NCBIEntrezData"]["human chromosome 10", "ESearch", "Database" -> "nucleotide", "IDType" -> "acc", "RetMax" -> 1]
Out[5]=

Use the ImportFASTA function to retrieve the DNA sequences from the latest as well as previous assemblies based on the converted coordinates:

In[6]:=
latestseq = StringTake[ ResourceFunction["ImportFASTA"][chr10acc["IDList"][1], "BioSequence"], ToExpression@ StringSplit[genomefeature[1, "Location"], ":" | "-"][[-2 ;;]]]
Out[6]=
In[7]:=
previousseq = StringTake[ ResourceFunction["ImportFASTA"][ StringSplit[chr10acc["IDList"][1], "."] /. {nc_String, ver_String} :> StringJoin[nc, ".", ToString[ToExpression[ver] - 1]], "BioSequence"], precoord]
Out[7]=

Find that sequences from both assemblies match:

In[8]:=
Diff[latestseq, previousseq]
Out[8]=

Requirements

Wolfram Language 13.0 (December 2021) or above

Version History

  • 1.0.1 – 21 April 2025
  • 1.0.0 – 17 April 2025

Source Metadata

  • Citation:
    • Peter W Harrison, M Ridwan Amode, Olanrewaju Austine-Orimoloye, Andrey G Azov, Matthieu Barba, If Barnes, Arne Becker, Ruth Bennett, Andrew Berry, Jyothish Bhai, Simarpreet Kaur Bhurji, Sanjay Boddu, Paulo R Branco Lins, Lucy Brooks, Shashank Budhanuru Ramaraju, Lahcen I Campbell, Manuel Carbajo Martinez, Mehrnaz Charkhchi, Kapeel Chougule, Alexander Cockburn, Claire Davidson, Nishadi H De Silva, Kamalkumar Dodiya, Sarah Donaldson, Bilal El Houdaigui, Tamara El Naboulsi, Reham Fatima, Carlos Garcia Giron, Thiago Genez, Dionysios Grigoriadis, Gurpreet S Ghattaoraya, Jose Gonzalez Martinez, Tatiana A Gurbich, Matthew Hardy, Zoe Hollis, Thibaut Hourlier, Toby Hunt, Mike Kay, Vinay Kaykala, Tuan Le, Diana Lemos, Disha Lodha, Diego Marques-Coelho, Gareth Maslen, Gabriela Alejandra Merino, Louisse Paola Mirabueno, Aleena Mushtaq, Syed Nakib Hossain, Denye N Ogeh, Manoj Pandian Sakthivel, Anne Parker, Malcolm Perry, Ivana Piližota, Daniel Poppleton, Irina Prosovetskaia, Shriya Raj, José G Pérez-Silva, Ahamed Imran Abdul Salam, Shradha Saraf, Nuno Saraiva-Agostinho, Dan Sheppard, Swati Sinha, Botond Sipos, Vasily Sitnik, William Stark, Emily Steed, Marie-Marthe Suner, Likhitha Surapaneni, Kyösti Sutinen, Francesca Floriana Tricomi, David Urbina-Gómez, Andres Veidenberg, Thomas A Walsh, Doreen Ware, Elizabeth Wass, Natalie L Willhoft, Jamie Allen, Jorge Alvarez-Jarreta, Marc Chakiachvili, Bethany Flint, Stefano Giorgetti, Leanne Haggerty, Garth R Ilsley, Jon Keatley, Jane E Loveland, Benjamin Moore, Jonathan M Mudge, Guy Naamati, John Tate, Stephen J Trevanion, Andrea Winterbottom, Adam Frankish, Sarah E Hunt, Fiona Cunningham, Sarah Dyer, Robert D Finn, Fergal J Martin, and Andrew D Yates
      Ensembl 2024 Nucleic Acids Res. 2024, 52(D1):D891–D899 PMID: 37953337

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