Hello Albert, The data display is for PSL data: http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#PSLDisplay
Basically, a region between blocks that looks like a real splice site is represented by a line with arrows in the direction of transcription. A region between blocks that does look like a splice site will also have arrows in the direction of transcription, but it will be boxed in (to simplify, if you see boxes, the query will often be non-contiguous across ordered exons). Jennifer --------------------------------- Jennifer Jackson UCSC Genome Bioinformatics Group http://genome.ucsc.edu/ On 2/17/10 7:19 AM, Albert Vilella wrote: > Hi, > > In displaying blat results, what is the difference between an arrow > that links two matches and a squared arrow? > > for example, in an image like this (also attached): > http://genome.ucsc.edu/trash/hgt/hgt_genome_7c20_c07d60.gif > > there is first left-hand side block of 7 matching sequences that is > linked by arrows, then squared links for the first 3, then the fourth > is an arrow, and the last 3 are squared links... etc > > what is the conceptual difference between arrows and squared links? > > Cheers, > > Albert. > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
