Question: GC content calculation for Genes
1
gravatar for Pranavathiyani G
4.1 years ago by
Pondicherry, India
Pranavathiyani G300 wrote:

I have a list of Human Genes(Gene Symbols: Eg-> PTEN, AASS, AATBC, AATF, QARS, ABAT, ACHE, etc), How can I find the GC content(%) of these genes? Is there any tool or database available? I don't want to calculate by taking each gene sequence & to find the GC content. Is there any alternative way, a tool?

cpg tool sequence database gene • 3.5k views
ADD COMMENTlink modified 4.1 years ago by Devon Ryan95k • written 4.1 years ago by Pranavathiyani G300

It has been already discussed in biostars.org

What Is The Gc-Content Across Different Human Chromosomes?

as well as in this paper:

http://courses.cs.washington.edu/courses/cse527/07au/notes/notes16.pdf

It was calculated for different chromosomes, but no tools were mentioned.

http://blog.kokocinski.net/index.php/gc-content-of-human-chromosomes?blog=2

ADD REPLYlink modified 4.1 years ago • written 4.1 years ago by natasha.sernova3.7k

I think that throughout the gene body and exon intron structure your GC value will differ widely and as such a GC content per gene will be a meaningless trait... perhaps (depending on what you want to do) a sliding window approach is more appropriate.

ADD REPLYlink written 4.1 years ago by WouterDeCoster43k

This is hugely important. You really need to be sure that the term "gene" is meaningful given the context of your experiment. Fortunately, that link Devon gave you makes it really easy to slice and dice your regions with the filters :)

ADD REPLYlink modified 4.1 years ago • written 4.1 years ago by John12k
5
gravatar for Devon Ryan
4.1 years ago by
Devon Ryan95k
Freiburg, Germany
Devon Ryan95k wrote:

Because I'm nice, here is the biomart URL with the result for all human genes.

ADD COMMENTlink written 4.1 years ago by Devon Ryan95k
1
gravatar for mastal511
4.1 years ago by
mastal5112.0k
mastal5112.0k wrote:

You can get %GC from Biomart.

ADD COMMENTlink written 4.1 years ago by mastal5112.0k
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