I just started learning the compara API. However, I am still not sure whether it can address my questions. I am wondering if someone could give me some guidance and example scripts.
Here is my question: (1) I want to identify in human genome all the DNA fragments that are significantly similar (homology, by lastZ or BlastZ). (2) Then, I want to find in which of the other species, two homology DNA fragments of human are significantly similar (aligned) to one genomic region in that species.
Alternatively, I can focus on two genomic regions in a genome to test if they are homologous and then which species has one genomic region that is aligned to both of the human genomic regions.
Particularly, I am wondering in the human self alignment, one genomic region may be mapped to multiple other regions. These multiple hits also exist in e.g. the mouse genome of the human vs mouse genome alignment. Does ensembl provide all these multiple regions or just the best one?
Any scripts that can achieve my goals? My compara API version is 95.