In trees of life, people have been using the degree of conservation to assign the branches. I am wondering where I can look up for the numbers representing the diversity or commonality between two species (such as zebrafish and human).
Also, another question is that "how do I find the regions that are not conserved between the two species?"
You can try an all genomes alignment with MAUVE. It will make link between conservation.
and then ofcourse there are a number of tools that can be used:
1. SyntTax
2. Cinteny Server for Synteny Identification and Analysis of Genome Rearrangement
3. AutoGRAPH
4. Sibelia
5. GeneOrder 2.0
6. CoreGenes
7. WebACT
8. WebGMAP
9. Panseq
links to these are available on:
http://molbiol-tools.ca/Genomics.htm
Also by looking at the numbers you somehow take into account the degree of conservation, because the grouping of proteins/genes into homologous or better in your case orthologous group requires taking that into account at some point. Take a look at this paper:
http://www.biomedcentral.com/1471-2164/12/32
where they develop a measure to describe how much fluid is the gene content between different strains of the same species and can thus be taken as an indication of the ease with which new genes are gained or old ones are lost in a given group of organisms. I think it has never been used for eucaryotes but in principle it should also work once you correctly address the orthologous classification problem.
There are several online databases where you can get the classification done and simply proceed with counting, the most known ones are cog and kegg (KO), but several others exist (e.g. HOGENOM at the Lyon University/PBIL http://pbil.univ-lyon1.fr/databases/hogenom/home.php)
- Badges
- Science topic
- Similar topics
- Biological Science
- Evolutionary Biology
- Phylogenetics