Question: Reference Genome of Saccharomyces cerevisiae S288C.
0
gravatar for midox
4.5 years ago by
midox260
Tunisia
midox260 wrote:

hello,
i would like the file of the reference genome of Saccharomyces cerevisiae S288C.
have you a link to download the file?

and what is the best tool for comparison to the reference genome?

Thankyou

ADD COMMENTlink modified 4.5 years ago by harold.smith.tarheel4.5k • written 4.5 years ago by midox260

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

ADD REPLYlink written 4.5 years ago by poisonAlien2.8k
0
gravatar for samuelmiver
4.5 years ago by
samuelmiver430
Centre for Genomic Regulation (Barcelona, Spain)
samuelmiver430 wrote:

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

ADD COMMENTlink modified 4.5 years ago • written 4.5 years ago by samuelmiver430
0
gravatar for harold.smith.tarheel
4.5 years ago by
United States
harold.smith.tarheel4.5k wrote:

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).

ADD COMMENTlink modified 5 months ago by RamRS27k • written 4.5 years ago by harold.smith.tarheel4.5k

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

ADD REPLYlink modified 5 months ago by RamRS27k • written 4.5 years ago by midox260

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).

ADD REPLYlink modified 5 months ago by RamRS27k • written 4.4 years ago by harold.smith.tarheel4.5k

thank you for your help.

but QUAST is used for assessing genome assemblies.

me, 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.

Is there other good tools?

ADD REPLYlink modified 5 months ago by RamRS27k • written 4.4 years ago by midox260

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

Do you mean sequence alignment? I would recommend BBMap.

ADD REPLYlink modified 5 months ago by RamRS27k • written 4.4 years ago by harold.smith.tarheel4.5k

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

ADD REPLYlink modified 5 months ago by RamRS27k • written 4.4 years ago by midox260

how to interpret the BBmap results?

I used BBmap but I did not understand the results.

Thank you

ADD REPLYlink modified 5 months ago by RamRS27k • written 4.4 years ago by midox260
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