Hi Brooke, > 1. what does '=' mean? > > "I -- there are non-aligning bases in the source species between chained > alignment blocks before and after this block. The browser shows a double > line or '=' in base mode." > > > 2. What does the number on the "Gaps" line mean? > > "n -- there are non-aligning bases in the source and the next aligning block > starts in a new chromosome or scaffold that is bridged by a chain between > still other blocks. The browser shows either a single line or a double line > based on how many bases are in the gap between the bridging alignments."
Sorry. I didn't see these two lines. "The browser ..." starts at the middle of the lines. Since these two start with the letters "I" and "n", I assume that the lines are just for explaining the meaning of these two letters, which is a reasonable assumption. I'd suggest to break each line into two lines, so that it will be more obvious to see the word "browser". However, I think that that an even better way is to add an section only explaining how browser displays. Although there will be more redundancy if the same information is explained twice, but it is easier for people looking for things. BTW, the document width is the same as the browser width. Nowadays, the LCDs are pretty wide and the browser can be also pretty wide. Each line is displayed too long, which is hard to read. Although people could make the browser windows smaller, a better strategy is to restrict the maximum line width. I'm wondering if this suggestion can be considered. In the "Gap Annotation" section at http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=230315893&c=chr21&g=cons46way(BTW, it is now 46 way instead of 44 way, the link that you given is broken), I don't understand the following two definitions. What are the difference between the two? Single line: no bases in the aligned species. Double line: aligning species has one or more unalignable bases in the gap region. For example, I copied the following alignment from the genome browser. Would you please explain what is the difference between '-' and '='? Human AATAAAAATACC Rhesus AATTAAAATACC Mouse ============ Dog AATAAAAATAT- Elephant ------------ Opossum ============ Chicken ============ X_tropicalis Zebrafish ============ Thank you very much! -- Regards, Peng _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
