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Reference Genome of Saccharomyces cerevisiae S288C.

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

assembly next-gen reference-genome
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updated by Ram Ram • written by midox midox

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

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written by poisonAlien poisonAlien

2 answers

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

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written by samuelmiver samuelmiver

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).

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updated by Ram Ram • written by harold.smith.tarheel harold.smith.tarheel

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

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updated by Ram Ram • written by midox midox

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).

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updated by Ram Ram • written by harold.smith.tarheel harold.smith.tarheel

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?

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updated by Ram Ram • written by midox midox

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

Do you mean sequence alignment? I would recommend BBMap.

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updated by Ram Ram • written by harold.smith.tarheel harold.smith.tarheel

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

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updated by Ram Ram • written by midox midox

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

Thank you

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updated by Ram Ram • written by midox midox

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