Hi Luvina, The genomewiki URL and your reply helps a great deal. Thanks. Regards, Jaaved
-----Original Message----- From: Luvina Guruvadoo [mailto:[email protected]] Sent: Monday, February 14, 2011 4:13 PM To: Jaaved Mohammed Cc: [email protected] Subject: Re: [Genome] Net and Chain explanation Hi Jaaved, For the net tracks, the boxes represent ungapped alignments and the lines represent gaps. For more information, please see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=dm3&g=netDroEre1. For chain tracks, the boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the query species assembly (in your example, the /D. erecta/ assembly) or an insertion in the /D. melanogaster/ assembly. Double lines represent more complex gaps that involve substantial sequence in both species. For more information, please see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=dm3&g=chainDroEre1. The arrows within the lines refer to strand orientation. The chains are displayed based on their start position. They do have scores, which you can see by clicking on a particular chain. Also, you can use the net track to see easily see the highest scoring chains. When the net track is in full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. More information on chain/net tracks can be found here: http://genomewiki.ucsc.edu/index.php/Chains_Nets. Please contact us again at [email protected] if you have any further questions. Best, Luvina --- Luvina Guruvadoo UCSC Genome Bioinformatics Group Jaaved Mohammed wrote: > 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) > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
