Reference Genome of Saccharomyces cerevisiae S288C.

Question

[midox]

Hello,

I would like the file of the reference genome of Saccharomyces cerevisiae S288C. Do you have a link to download the file? And what is the best tool for comparison to the reference genome?

Thank you

[poisonAlien]

For all sort of resources on S.cerevisiae, you can always check SGD. Here is link to S288c ref genome on sgd.

Answer 1

[samuelmiver]

http://www.ncbi.nlm.nih.gov/genome/?term=Saccharomyces%20cerevisiae%20S288C

to compare two genomes I really like ACT (Artemis Comparison Tool)

http://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act

Answer 2

[harold.smith.tarheel]

The UCSC reference genome sacCer3 (available here) is S288c. Useful genome comparison tools are LAST and QUAST (more typically used for assessing genome assemblies, but also good for comparisons).

[midox]

There are several data (files) to the reference genome. Do I need to do a file comparison file? Or is that there is only one file to make the comparison?

Thank you

[harold.smith.tarheel]

If you select the link 'Full Data Set' you'll get a description of the different files. The reference is chromFa.tar.gz. After downloading and extracting, you may need to concatamerize the individual chromosome files (depending upon your comparison tool).

[midox]

Thank you for your help but QUAST is used for assessing genome assemblies. I have a file of reads and I would do the comparison of these reads to the reference to see the percentage of the identity of these reads to the reference. Are there other good tools?

[harold.smith.tarheel]

Your original post asked for genome comparison tools; that's what was provided.

Do you mean sequence alignment? I would recommend BBMap.

[midox]

yes, I have w file of reads and I would like to do a comparison of these reads to the reference genome.

[midox]

How to interpret the BBmap results? I used BBmap but I did not understand the results.

Thank you