Hello,
I'm having difficulties understanding what the nets and chains mean for a particular species. The help text on the individual species nets/chains is still uninformative. I'm working primarily with the insect 15-way alignment and would like to get an understanding about how much confidence to given to homologous sequences that appear questionable in the multiple alignment. I was advised that the best way to understand this would be to examine the nets and chains on the browser. Here is my scenario: Starting off by querying any drosophila melanogaster coordinate (say chr2L:6,045,627-6,045,713) on the browser I manually add the chain and net tracks for D. erecta (as an example). I get the attached screenshot output for the above coordinate. Here are my particular questions: 1. On the nets track, say for D. erecta, what are the differences between single lines, double lines, and solid boxed lines? Also what does the arrows inscribed on the lines represent? 2. In the net for a species, what do the levels mean? I'm having difficulties understanding why a solid box occurs in level 2 vs. a single line ( which I think is a gap) occurring on level 1. 3. I see multiple sequences on the chain track for a particular melanogaster coordinate. Are these "chains" ranked by some sort of score or are they any coordinates in ereta that has synteny with the melanogaster sequence with no particular ordering? Thanks in advance for your help. Regards, Jaaved -- Jaaved Mohammed, Ph.D. Student of Computational Biology Tri-Institutional Training Program in Computational Biology and Medicine (Cornell University - Ithaca, Weill Cornell Medical College, and Memorial Sloan-Kettering Cancer Center)
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