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closeEffect of GC content?
Posted by DixieMager on 21 Jan 2010 at 00:28 GMT
It is well known that Alus and B1s are enriched in regions of high GC content. Perhaps the functional gene classes associated with higher densities of these elements are also high in GC content. It would be interesting to normalize for GC content to see if the results change.
RE: Effect of GC content?
aristotelis replied to DixieMager on 22 Jan 2010 at 21:26 GMT
ALUs are GC-rich (~51%) compared to the overall human genome GC content (~41%). Now, if you take the areas surrounding ALUs in the genome by 100nt up/downstream (and exclude the ALU sequences themselves from the computation), you will find that the GC content is ~37%. For 1000nt, GC content increases to 40% approaching the genomic average.
Given these observations, I would rather say that ALUs are GC-rich and are surrounded by AT-poor regions. In any case I would be happy to continue this interesting discussion, so feel free to e-mail me at atsirigo@us.ibm.com.
RE: RE: Effect of GC content?
aristotelis replied to aristotelis on 18 Apr 2010 at 19:20 GMT
Small, but important correction in my previous posting: I meant to say that ALUs are surrounded by AT-rich regions, not AT-poor.