Adding new species to available genome assemblies

[Aaron Hernday]

Hello,

 

I’m interested in using some of the tools in your Expasy suite, but noticed that the organism that I work with (Candida albicans) is not included in the list of available genomes. Is it possible to have this added? I’ll be happy to provide whatever files are needed from the Candida Genome Database (we typically use assembly 21, since it is the most up to date haploid assembly for C. albicans).

 

Please let me know if this is possible, and how I can best assist.

 

All the best,

Aaron

 

Aaron D. Hernday

 

Associate Professor

MCB Department

UC Merced

5200 N Lake Rd

BSP rm 479

Merced, CA

95343

 

Office: (209) 228-2450

Website: https://sites.ucmerced.edu/hernday-lab-ucm

 

[CCG EPFL]

Dear Aaron, 

Thanks for your interest in EPD.

Yes, it appears feasible to produce an EPD module for Candida albicans. But first, please confirm that 

the source data we are planning to use are appropriate for this purpose: 

Candida Genome Database: 

NCBI genome:

https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/032/688/725/GCA_032688725.1_ASM3268872v1/

GenArk genome browser:

https://genome.ucsc.edu/cgi-bin/hgTracks?genome=GCA_032688725.1&hubUrl=/gbdb/genark/GCA/032/688/725/GCA_032688725.1/hub.txt

TSS mapping data:

McMillan J, Lu Z, Rodriguez JS, Ahn TH, Lin Z.
YeasTSS: an integrative web database of yeast transcription start sites.
Database (Oxford). 2019 Jan 1;2019:baz048.
doi: 10.1093/database/baz048. PMID: 31032841; PMCID: PMC6484093.

Raw data links:

 

https://www.ncbi.nlm.nih.gov/sra/SRX5170939
https://www.ncbi.nlm.nih.gov/sra/SRX5170938

The generation of the database will take some time (perhaps 2 month). We will contact you if we have questions. Don't hesitate to contact us from time to time for a status update or with particular suggestions regarding the contents and design of the viewer.

Best wishes,

Philipp