Is there such a file in which, the human-mouse syntenic regions are listed one to one, correspondingly? I need all the syntenic regions between human and mouse. If there is no such file, how can I generate one?
To define blocks of synteny you need to know resolution of your analysis, E.g., at high resolution you'll have a lot of small blocks while at low resolution you will see larger blocks but they will contain small rearrangements inside. You can take a look at synteny between human and mouse at our site http://eh-demo.ncsa.uiuc.edu (Java required) If you prefer to define your own blocks using your own criteria you can do this using our other tool: http://www-app.igb.uiuc.edu/labs/lewin/donthu/Synteny_assign/html/
I don't know. The Double-ACT genome comparison tool ( http://www.hpa-bioinfotools.org.uk/pise/double_act.html ) does not state that it is only for bacterial chromosomes, plasmids, viruses and other small genomes. But I suspect that it is only useful when the input genomes or genome regions are already known to have some synteny.
This paper:
http://genome.cshlp.org/content/10/9/1351.long
The Syntenic Relationship of the Zebrafish and Human Genomes
compared the human a zebrafish genomes, so the authors can probably give you a lot better help than I can give you.
To define blocks of synteny you need to know resolution of your analysis, E.g., at high resolution you'll have a lot of small blocks while at low resolution you will see larger blocks but they will contain small rearrangements inside. You can take a look at synteny between human and mouse at our site http://eh-demo.ncsa.uiuc.edu (Java required) If you prefer to define your own blocks using your own criteria you can do this using our other tool: http://www-app.igb.uiuc.edu/labs/lewin/donthu/Synteny_assign/html/
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