When zoomed-in to the base-level display, the track shows the base composition of each alignment. The numbers and symbols on the Gaps line indicate the lengths of gaps in the $organism sequence at those alignment positions relative to the longest non-$organism sequence. If there is sufficient space in the display, the size of the gap is shown. If the space is insufficient and the gap size is a multiple of 3, a "*" is displayed; other gap sizes are indicated by "+".
Codon translation is available in base-level display mode if the displayed region is identified as a coding segment. To display this annotation, select the species for translation from the pull-down menu in the Codon Translation configuration section at the top of the page. Then, select one of the following modes: @@ -143,30 +135,59 @@ scores reflect the phylogeny (including branch lengths) of the species in question, a continuous-time Markov model of the nucleotide substitution process, and a tendency for conservation levels to be autocorrelated along the genome (i.e., to be similar at adjacent sites). The general reversible (REV) substitution model was used. Note that, unlike many conservation-scoring programs, phastCons does not rely on a sliding window of fixed size, so short highly-conserved regions and long moderately conserved regions can both obtain high scores. More information about phastCons can be found in Siepel et al. (2005).
PhastCons currently treats alignment gaps as missing data, which sometimes has the effect of producing undesirably high conservation scores in gappy regions of the alignment. We are looking at several possible ways of improving the handling of alignment gaps.
++The alignments and the conservation scores can be retrieved for a single region or for a list of +regions with the Table Browser, +which returns the alignments in MAF format and the scores as wiggle data. The scores and the +conserved elements, though not the alignments, can also be joined with other annotations in the +Data Integrator. For automated access, our REST API serves the alignment and conservation tracks +individually, by name. +
++Downloads for data in this track are available: +
+Genome-wide alignment files are large. Among our command-line programs, mafsInRegion, +mafSpeciesSubset and mafFrags pull out a region, a subset of species, or the +alignment underlying a gene. They can be downloaded from the utilities directory, and +each one prints its usage when run with no arguments. See our Data Access FAQ for more information. +
+This track was created at UCSC using the following programs: