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I'm trying to find some reference that shows what percentage of the human genome is similar to some organism from the domain Archea that lives near or on deep sea hydrothermal vents.

Can someone points me out in the right direction?

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    $\begingroup$ The genomes are so different that it is pretty impossible to make any alignment expect for few very conserved region. I guess that you may be able to align histone genes eventually ribosomes (although they differ a lot). You may want to find these sequences and align them by yourself for training. $\endgroup$ – Remi.b May 1 '15 at 23:54
  • $\begingroup$ @Remi.b I am curious, but would alignment of these genomes be done by some BLAST like program? $\endgroup$ – Ro Siv May 2 '15 at 0:15
  • $\begingroup$ @Ro Siv Yes, exactly. $\endgroup$ – Remi.b May 3 '15 at 15:11
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To achieve whole genome alignment between a genome as large as a human, and as small as an archea organism, is possible, but in the end, you'll have to strain your eyes to see patterns. The archea genome is about 1-5 million bp long, whereas the human genome is about 3.3 billion bp long (that's a thousand times too large).

In practice what this means is that you may or may not have small islands of similarity, in vast regions of emptiness.

Nevertheless, you can align whole genomes using the MUMer tool (http://mummer.sourceforge.net/). The white paper is here Delcher, Arthur L., et al. "Alignment of whole genomes." Nucleic acids research 27.11 (1999): 2369-2376.

You might also be interested in reading this:

Wei, Liping, et al. "Comparative genomics approaches to study organism similarities and differences." Journal of biomedical informatics 35.2 (2002): 142-150.

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