Gene therapy and its connection to evolution

signal sequences with tolerable errors that can tolerate "slight" inconsistencies but eventually lead to untolerable mutations that lead to phenotypic change
 
Yes my gene was correct. If I got some more time I'd be interested in testing more sequences. Sequences around genes are not totally random of course as they are specific singals important for transcription translation and regulation of the genes. I am somewhat surprised that small strings did work, though.
Regarding your hypotheses, I am not quite sure what you mean. The consistency between conserved genes is nothing surprising. But why do you suppose that they evolved independently several times? The genes you have given are surely orthologs (that is, derived from the same ancestor)?
As such of course the surrounding regulatory elements are also conserved.
 
Evolution is like a tree right ... starts with small unicelled and end up with totaly different species ... who evlolve separete one from another.
Any way if you whan to try more genes ... just open the big text file I've linked - it has all the gene_inexes on all the genomes I have. the small text file has only the genes with matching gene_indexes ... both files are sorted.
 
cyber_indian said:
"Hercules Rockefeller", "CharonZ" :) How's the result goning for you ?
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As for CharonZ, your result was correct.

Having said that, I have to concur with the puzzlement of the other posters in this thread. :confused:

In one way or another, I deal with gene sequences and gene sequence databases almost every day, yet I cannot comprehend any relevance or usefulness to what you are doing. You have simply listed all the “gene indexes” for a given set of genomes, and then proposed to identify a given gene when supplied with any of the gene indexes that you have cataloged.

The huge amount of work and computer database programming required to do this notwithstanding, my response is: “So what?” :eek:

What biological problem would necessitate such an approach? Under what circumstances will a scientist have the last 9 bases and 5’ UTR sequence and the first 9 bases of 3’ UTR sequence yet not know what the gene is?


cyber_indian said:
And what do you make of such consistency between all posible genes ? Is it accidental ? "Natural Selection" - "Evolution" ?!?!?! How did it happened - having different species separete one from another and still they evolove new genes - separate, but still there is consistency between those genes ??? Explain me that.
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Your puzzlement puzzles me! You have identified the answer to our question already. It is explained easily by a theory known as “evolution”. This theory explains the consistency and similarity in gene sequences perfectly – all organisms have evolved from a common ancestor. It’s as simple as that, really.
<P>
 
cyber_indian said:
Evolution is like a tree right ... starts with small unicelled and end up with totaly different species ... who evlolve separete one from another.
Any way if you whan to try more genes ... just open the big text file I've linked - it has all the gene_inexes on all the genomes I have. the small text file has only the genes with matching gene_indexes ... both files are sorted.
Click to expand...

Wrong. We no longer consider the tree of life to be grounded in a single common ancestor. It is now thought to be a ring composed of yeasts, proteobacterium, cyanoacterium, halobacterium, eocyte, and bacillus that, in combination, gave rise to bacteria, archae, and eukaryotes. How can you resolve that with your singular seperate genome theory?
 
About the "huge amount of work" I enjoy busting computers ass, I have dual Xeon and two 8 CPU servers and etc. As for "relevance or usefulness" I guess nobody is realy listneing and I guess I have to make a page and picture why are those gene_indexes there. For now I can say is that gene_index is for instance the answer to the pathogeninc outcome to the "gene therapy" methods.
As for "theory explains the consistency and similarity" - let say you have orange and dog each one evolve one new gene that had noting to do with eachother, now how do you make sure that orange_new_gene and dog_new_gene don't have the same gene_index - "having different species separete one from another and still they evolove new genes - separate, but still there is consistency between those genes".
 
Nobody realy intrested why there are gene_indexes, Nobody want to speculate the posible explanation ? That what puzzles me ...
 
That's the answer

AAAAGAACAxTGGTATTTA|347bp|10F134E82DDAAFB9|+|E|ND3|NC_006930_1|NADH dehydrogenase subunit 3|
AAAAGAACAxTGGTATTTA|347bp|5419766E7095B157|+|E|ND3|NC_006927_1|NADH dehydrogenase subunit 3|
AAAAGAACAxTGGTATTTA|347bp|7C253578584EAA6E|+|E|ND3|NC_006929_1|NADH dehydrogenase subunit 3|
AAAAGAACAxTGGTATTTA|347bp|CBC2A35D05FCD8C4|+|E|ND3|NC_006931_1|NADH dehydrogenase subunit 3|
AAAAGAACAxTGGTATTTA|347bp|D8ACFE0A2774782F|+|E|ND3|NC_006928_1|NADH dehydrogenase subunit 3|

AAAAGAATAxTGGTATTTA|347bp|C0F1502CD77389D3|+|E|ND3|NC_006993_1|NADH dehydrogenase subunit 3|
AAAAGAATAxTGGTATTTA|347bp|F1B4DB2951F33B51|+|E|ND3|NC_006973_1|NADH dehydrogenase subunit 3|

AAACGTCTAxGTCTTTCTA|785bp|138F4F4FDCB90469|+|E|COX3|NC_006918_1|cytochrome c oxidase subunit III|
AAACGTCTAxGTCTTTCTA|785bp|C07784123B237A18|+|E|COX3|NC_002646_1|cytochrome c oxidase subunit III|
AAACGTCTAxGTCTTTCTA|785bp|DE292D8626291116|+|E|COX3|NC_005799_1|cytochrome c oxidase subunit III|

AAACTGACCxATGGCCCAC|682bp|68A3FFF8570775DF|+|E|ATP6|NC_001708_1|ATP synthase F0 subunit 6|
AAACTGACCxATGGCCCAC|682bp|E957AF1C62237E48|+|E|ATP6|NC_004593_1|ATP synthase F0 subunit 6|
AAACTGACCxATGGCCCAC|683bp|9A3082D7686A503B|+|E|ATP6|NC_006918_1|ATP synthase F0 subunit 6|
AAACTGACCxATGGCCCAC|683bp|D5F34804CD791F7C|+|E|ATP6|NC_006919_1|ATP synthase F0 subunit 6|

AAACTGATCxTTTCATGTT|502bp|8A36CA8A51A311EB|+|E|F15E11.13|NC_003283_4||
AAACTGATCxTTTCATGTT|502bp|8A36CA8A51A311EB|-|E|Y19D10B.7|NC_003283_4||

AAATATACAxTTTATCAAT|1439bp|6CF4D17749AB07FA|+|E|Y49F6A.2|NC_003280_3||
AAATATACAxTTTATCAAT|1439bp|6CF4D17749AB07FA|-|E|Y49F6A.3|NC_003280_3||

AAATTGAAAxATGTCTACA|674bp|69D6D1DF60C49BDF|+|E|ATP6|NC_005779_1|ATP synthase F0 subunit 6|
AAATTGAAAxATGTCTACA|674bp|9DE01C9BE9B2BBBA|+|E|ATP6|NC_005780_1|ATP synthase F0 subunit 6|

AACGCTCGAxAGAACGGAT|2418bp|14E9C930D5EA8768|-|E|K10F12.5|NC_003281_4||
AACGCTCGAxAGAACGGAT|2418bp|A500B36AEB1DF644|+|E|Y102A11A.4|NC_003284_4||

Just look in the two text files and see for yourself - They are sorted for easy review and the second file has only the matching gene_indexes
 
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But it's still normal to have problems with more complex genes ... If you have got what is my idea you'll know that these gene_indexes are not used to identify genes, but to guide where exatly a target cDNA (gene) should be attached, by matching gene_index with the target chromosome - sticky ends. Meaning that the gene_index should be at both ends (half front, half back) of the cDNA and that a more complex structures may not exactly match the begining and the end of that gene.
But still can be used to pair genes by functionality.
 
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