Hello Albert, I made a small but very important typographical error in my first response. Please read this one instead. Notice the capitalized "*NOT*". Very sorry for the confusion.
----- 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 *NOT* 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). To add a bit more, the boxed regions can signal a "double-gap", where there is mRna sequence data present, and reference genome sequence data present, but they do not align (match). The main point about the boxes is that they signal that something more complex is going on with the alignment. Clicking through to view the actual blocks would be advised to determine exactly what type of rearrangement there is. Jennifer On 2/17/10 9:42 AM, Jennifer Jackson wrote: > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
