Hi Albert, Your question has generated a bit of discussion here - so much that we felt it was necessary to be clearer when explaining what the alignment display exactly represents. The change to the Help document is not published yet, but this is a draft of what we will be amending. If you have any questions or input, we would welcome the feedback.
Jennifer ---- draft help for psl display ---- Pat space layout (PSL) alignment tracks: Aligning regions (usually exons when the query is cDNA) are shown as black blocks. In dense display mode, the degree of darkness corresponds to the number of features aligning to the region or the degree of quality of the match. In pack or full display mode, the aligning regions are connected by lines representing gaps in the alignment (typically spliced-out introns), with arrowheads indicating the orientation of the alignment, pointing right if the query sequence was aligned to the forward strand of the genome and left if aligned to the reverse strand. Two parallel lines are drawn over double-sided alignment gaps, which skip over unalignable sequence in both target and query. For alignments of ESTs, the arrows may be reversed to show the apparent direction of transcription deduced from splice junction sequences. In situations where no gap lines are visible, the arrowheads are displayed on the block itself. To prevent display problems, the Genome Browser imposes an upper limit on the number of alignments that can be viewed simultaneously within the tracks image. When this limit is exceeded, the Browser displays the best several hundred alignments in a condensed display mode, then lists the number of undisplayed alignments in the last row of the track. In this situation, try zooming in to display more entries or to return the track to full display mode. For some PSL tracks, extra coloring to indicate mismatching bases and query-only gaps may be available. --------------------- --------------------------------- 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
