Question

Comparative Genome Analysis vs. Comparative Genomics

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4.0 years ago

pfee418 ▴ 10

Hi everyone, I'm new to the field of comparative analysis. May I know the difference between comparative genome analysis and comparative genomics? Are they similar?

Apart from that, I learnt that researchers sometimes will do multiple sequence alignment (MSA) on the sequences and find difference between the sequences. May I know what techniques or methods the researchers used to identify the differences among the aligned sequences? I tried to find the methods from the published articles but many similar articles never stated on how they find out the differences, any experts/professionals that knew bout this can explain to me about this? actually I'm kinda lost bout this *sob sob*

Thank you in advanced for all the explanations and I will appreciate all the responses. :)))

comparativegenomics comparativegenomeanalysis • 1.3k views

ADD COMMENT • link written 4.0 years ago by pfee418 ▴ 10

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First of all this is a very general question or approach. It is a huge area. you can compare many part of genomes. briefly, the two statements intend to find similar/dissimilar part of genomes. For instance, you can compare; 1. genome structures: coding/non-coding part, length, same elements, size etc. 2. gene structure: number and size of genes, introns, axons. 3. evolution of some part of genomes: gene duplications, gene family expansion/contractions or gain/lost

@techniques or methods the researchers used to identify the differences among the aligned sequences? ; They do , as you say, multiple sequence alignment by using some tools such as mafft, muscle. They select, for instance, a gene which is found in genomes of species that they are interested in, and they use those tools whether any conserved sites, indels (insertion/deletions) in the gene. Lets say several amino acids of the gene may have been evolved in a species, and the evolved part (different amino acids) may be involved in a specific motif that is unique to that gene, meaning the key part of the gene for its function. If you want to answer a scientific question which is related to or based on evolution of a gene, you may further need to do selection analyses (positive selection or relaxed selection) that may have occurred on some specific amino acid sites of the gene.

ADD REPLY • link 4.0 years ago by Mehmet ▴ 820

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Oh I see. Thank you for the explanations. :) May I know which tools they will be using to search for conserved sites and indels? Because this is the thing I'm searching for my project, and it's quite hard to find as some articles did not stated about this at all (tools or techniques they used to search the conserved sites and indels).

ADD REPLY • link 4.0 years ago by pfee418 ▴ 10

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A short description:

https://en.wikipedia.org/wiki/Conserved_sequence