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strand biases in mitochondrial genomes

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strand biases in mitochondrial genomes

Postby smack » Mon Jun 27, 2011 1:07 pm

Hi,

i have a research in bioinformatics and i need your help in some questions
i want to know what's useful in studying strand biases in mitochondrial genomes?? and why this study is well known these days??

why it's important to analyses these biases??

what it does help the scientist to resolve ??

i need some notes and comments about this subject.

thanks in advance
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Postby JackBean » Mon Jun 27, 2011 4:21 pm

I would imagine some phylogenetic studies
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.
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Re: strand biases in mitochondrial genomes

Postby smack » Mon Jun 27, 2011 10:49 pm

thnx for your reply, but is there any other ideas?? or more important things??
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Postby verginov » Wed Sep 21, 2011 11:51 am

The asymmetric strand biases in the genomes (including mitochondrial) directly impact the nucleotide composition of the genes, thus leading to different amino acid composition of the encoded proteins. As I understand you correctly, you have to search for a STRAND biases - different GC content in the two DNA strands of concrete mitochondrial genome.
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Postby merv » Sun Oct 02, 2011 6:06 pm

I dont know. have you read

http://dnaresearch.oxfordjournals.org/c ... 5/201.full
?

mitochondria have residual genomes. many of their genes, all of bacterial origin (see the endosymbiotic origin of organelles), have been transferred to the host genome.
Several diseases of metabolism are related to disabled genes in the mitochondrial genome. These are mainly of maternal origin, as sperm mitochondria are in the tail of the sperm which rarely enter the egg.
You ask about strand bias- if i understand you correctly, you mean what is termed GC skew - this is very odd terminology - as G always pairs with C with the exception of the temporary induction of mispaired mutations. GC skew means more G's on a strand than C's - and it impacts upon the codon usage - see the redundancy in the genetic code - remember that the third base pair of every 3bp codon is more often than not redundant- and is therefore neutral in simple terms - but as some tRNA's are more efficient than others, modification of the third base can have differences in the efficiency of protein production. So control of gene expression is a good answer - i don't think any of skews can be linked to disease states yet, it would be interesting to know....anyone?

On a different but related note, GC content may be variable % and not exactly 50%. This is a different issue but it is easy to confuse the two...just for the record then, some genomes are much higher in GC than AT. The reasons for this I think are still unknown.
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