Talk:GC-content

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Untitled

I have merged this article with Guanine-cytosine content. Hopefully I managed to do it properly. --Chino 10:34, 7 Mar 2005 (UTC)

GC content and temperature

The last part of the last sentence of the first paragraph: "[...], and thus GC-content tends to be greater in hyperthermophiles." is not supported by data (see Galtier and Lobry, 1997). I would suggest something like "One may think that having a high G+C content is selectivley advatageous for hyperthermophiles, but this is not the case (Galtier and Lobry, 1997)."

Galtier, N. and Lobry, J.R. (1997). "Relationships between genomic G+C content, RNA secondary structure, and optimal growth temperature in prokaryotes". Journal of Molecular Evolution. 44: 632–636.{{cite journal}}: CS1 maint: multiple names: authors list (link)

Genome is asymmetric

The last sentence of the third paragraph states that "In many prokaryotic organisms the genome is asymmetric: the composition of the strand being continuously replicated (leading strand) and its complementary (lagging strand) show different GC-contents.". This is not true, the GC-content is always the same in the two DNA strands. I think there is a confusion here with the GC-skew and the AT-skew (see Lobry 1996). I think that this sentence should be deleted from the "GC-content" article.

Lobry, J.R. (1996). "Asymmetric substitution patterns in the two DNA strands of bacteria". Molecular Biology and Evolution. 13: 660–665.

86.216.213.183 16:24, 18 August 2006 (UTC)[reply]

I was reading the article and was confused by this sentence, since the article is about paired GCs. The ext link given in the sentence wasn't too helpful, but the (G-C)/(G+C) formula there made it clear the subject was something else. This link I found is a bit more enlightening, and makes it clear the subject is not the same as GC-content. I've removed the sentence. It would be good to have a separate article about GC-skew. -R. S. Shaw 04:17, 30 September 2006 (UTC)[reply]

AT/GC ratio

I created an entry on G+C ratio yesterday but it was not till this morning did I realise that a GC content entry exists here. But although GC content and AT/GC ratio are similar, I think they are not the same, since GC content is expressed in % values but AT/GC is a ratio. I would like to know if these two entries can stay independent or should be merged. Thanks ώЇЌĩ Ѕαи Яоzε^†αLҝ 11:52, 10 June 2007 (UTC)[reply]

It looks like a nice article you started, but I'm pretty sure they should be merged. Debivort 17:58, 10 June 2007 (UTC)[reply]

Thanks Debivort! Yes I will merge the entries. I just need some advice on the same.

I'm I right in saying that the G+C ratio is not the same as GC-content, ie, values of GC-content will be different to G+C ratio (which is A+T/G+C). In that case should I make it as one of the sub under GC content?

Which picture stays? I personally feel that one in G+C ratio now fits into the topic. But I may carry a bias since I made it (LOLZ). In case we are staying with current double strant picture, I can delete the earlier.

Thanks! ώЇЌĩ Ѕαи Яоzε^†αLҝ 19:13, 10 June 2007 (UTC)[reply]

yeah ... I'd say use your image, which is more specifically related, and move ratio-specific text into a section of this article. I guess then G+C ratio should redirect here. Probably all sorts of other article names too, like GC ratio G/C ratio GC content G+C content G/C content, dontcha think? Let me know if you want help with the transfer. Debivort 19:21, 10 June 2007 (UTC)[reply]

Cheers Debivort! I would try to copy edit the entry through the week, but before that we should agree on the sections that are to be under GC content, since that would make it easier for the copy edit process. Any suggestions? Since I got a thesis to write too (poor me!!), I would appreciate any help from you. :-) ώЇЌĩ Ѕαи Яоzε^†αLҝ 19:31, 10 June 2007 (UTC)[reply]

How about:

GC content intro
measures of GC content (ratio)
genome wide GC conent

ecological impact
thermophiles

coding sequence-level variation in GC content
experimental determination of GC content

Thesis eh? I have one of those to write too. Defending in September, theoretically. Debivort 20:14, 10 June 2007 (UTC)[reply]

Thanks! Makes sense. Mine probably in September too. Who knows anyways!!! ώЇЌĩ Ѕαи Яоzε^†αLҝ 21:45, 10 June 2007 (UTC)[reply]

Merge looks good Wikiality - nicely done. Debivort 20:48, 11 June 2007 (UTC)[reply]

Thanks Debivort! ώЇЌĩ Ѕαи Яоzε^†αLҝ 21:32, 11 June 2007 (UTC)[reply]

In spite of the higher thermostability conferred to the genetic material, it is envisaged that cells with high GC DNA undergo autolysis, thereby reducing the longitivity of the cell per se.

Could someone please clarify this? To say the cells are envisaged to undergo autolysis introduces ambiguity (are they observed to undergo autolysis? or merely thought to?). And what exactly happens to these cells? And why?

Thankyou! Asd28 08:45, 11 October 2007 (UTC)[reply]

Autolysis is observed in Pseudomonas species, and hence thought that it may be true with other cells too. Cheers ώiki Ѕαи Яоzε^†αLҝ 08:50, 11 October 2007 (UTC)[reply]

In the section of the formulae, I think the correct term is AT/GC ratio, not GC ratio or G+C ratio. GC-ratio is given in % and I think it is the same as GC-content, but different from AT/GC-ratio. This should be clarified.--Miguelferig (talk) 22:30, 17 July 2013 (UTC)[reply]

Effect on mutation rate

Hey all. I don't have time to incorporate this right this second, but this could be of interest: [1]. Darkfrog24 (talk) 18:18, 24 May 2010 (UTC)[reply]

Does this follow?

"GC ratios and coding sequence

Within a long region of genomic sequence, genes are often characterised by having a higher GC-content in contrast to the background GC-content for the entire genome. Evidence of GC ratio with that of length of the coding region of a gene has shown that the length of the coding sequence is directly proportional to higher G+C content.[13] This has been pointed to the fact that the stop codon has a bias towards A and T nucleotides and thus the shorter the sequence the higher the AT bias.[14]"

Apart from the whole paragraph being rather confusingly worded, it seems unlikely that compulsory A+T-biased stop codons (and while we're at it, the Start codon ATG has the same bias), would be the sole cause of a measurable length/GC relationship on anything over a few tens of codons. —Preceding unsigned comment added by 88.110.180.117 (talk) 09:39, 11 November 2010 (UTC)[reply]

Influence of GC content on PCR experiments

High GC stretches within a genome not only influence primer annealing temperatures; high-GC also leads to the formation of stable secondary structures, which makes e.g. sequencing of such regions quite difficult. Even modern high-throughput sequencing technologies include a PCR amplification step, and GC-rich DNA results in lower amplification efficiencies. For gene expression studies (RNA-Seq, based on sequencing of mRNA) or metagenomics, this might result in additional biases. See e.g. [2] for a publication describing this effect (in this case, a metagenome dataset). —Preceding unsigned comment added by 84.61.157.104 (talk) 23:04, 31 March 2011 (UTC)[reply]

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Merge suggestion

I think that GC skew should probably be merged into GC-content, since one is a subset of the other. There's quite a bit of duplicate content, and a lot of GC skew would make more sense in the context of the GC-content article. Any other opinions? T.Shafee(Evo&Evo)^talk 02:20, 3 June 2017 (UTC)[reply]

These are orthogonal notions from a mathematical point of view, I disagree with the assertion stating that GC skew is a subset of GC-content, this is pure nonsense 90.14.59.170 (talk) 21:01, 9 August 2017 (UTC)[reply]

Although I agree that content and skew are mathematically disctinct concepts, From what I know of the field, the only reason that people are interested in GC-content is to detect GC-skew. T.Shafee(Evo&Evo)^talk 04:01, 1 October 2017 (UTC)[reply]

Please no, GC content was used about 50 years before GC skew was discovered, and is still an usefull notion.90.53.34.81 (talk) 19:28, 4 November 2017 (UTC)[reply]

Though I appreciate the statement that GC skew is very closely related with GC content, I do not think that I see so much overlap between them that they should be merged. In particular, I disagree that people are interested in GC content only because they want to detect GC skew. There are many people who study GC content for other purposes. Additionally, GC skew is likely affected by the biases caused by the difference in the use of DNA replication system, whereas there are many more factors that could influence GC content of genome. — Preceding unsigned comment added by Genomebuffalo (talk • contribs) 05:48, 17 January 2018 (UTC)[reply]

I've now removed the merge suggestion tag from the articles. T.Shafee(Evo&Evo)^talk 05:13, 9 April 2018 (UTC)[reply]