what does "conservation of contiguity between homologous segments" mean?

Question

[13520805896]

Hi, I am new comer in bioinformatics.

I have a question when reading a review of Susana Vinga, 2003:

Genetic recombination and, in particular, genetic shuffling are at odds with sequence comparison by alignment, which assumes conservation of contiguity between homologous segments

I am confused about the concept of "contiguity", and

why should we assume "conservation of contiguity" in alignment?

Thanks!

Answer 1

[Devon Ryan]

You have to assume continuity, because if you didn't, then you're saying that the entire reference sequence can be randomly shuffled. If that's the case, no conceivable algorithm could produce confident alignments. You could still de novo assemble, of course.

[13520805896]

I am terribly sorry that I made a big mistake: it should be "contiguity" instead of "continuity", but your comment still gives me many helpful hints. Thank you!

And I think "contiguity" here just means continuous segments.

[Devon Ryan]

Contiguity means continuity, only in the sense of physical things being next to each other. An example would be, "the 48 contiguous states," which would be all of the US states except for Alaska and Hawaii, since the latter don't border any other state.

[13520805896]

Thank you very much for your help and your time! Really appreciate it!