Description
The $Organism mRNA track shows alignments between viral mRNAs
in Genbank and the $Organism draft sequence. Aligning regions (usually exons)
are shown as black boxes connected by lines for gaps (spliced
out introns usually). In full display, arrows on the introns
indicate the direction of transcription.
Method
Genbank viral mRNAs are aligned against the $Organism draft sequence using the
blat program (translated alignments).
These alignments are not filtered (as they usually would be
for vertebrate genomes) because viruses evolve so quickly and there
is much greater variance.
Using the Filter
The track filter can be used to change the color or include/exclude a subset of individual
items within a track. This is helpful when many items are shown in the track
display, especially when only some are relevant to the current task. To use the
filter:
- Enter a value in one or more of the text boxes to filter the mRNA display. For
example, to apply the filter to all liver mRNAs, type "liver" in the
tissue box. For a list of permissible filter values, consult the non-positional table in
the Table Browser that corresponds to the factor on which you wish to filter. For
example, the non-positional table "tissue" contains all of the types of tissues
that can be entered into the tissue text box. Wildcards can also be used in the
filter.
- If filtering on more than one value, choose the desired combination
logic. If "and" is selected, only mRNAs that match all of the filter criteria will
be highlighted. If "or" is selected, mRNAs that match any 1 of the filter criteria
will be highlighted.
- Choose the color or display characteristic that will be used to highlight or
include/exclude the filtered items. If "exclude" is chosen, the browser will not
display mRNAs that match the filter criteria. If "include" is selected, the browser
will display only those mRNAs that match the filter criteria.
When you have finished configuring the filter, click the Submit button.
Credits
The $Organism mRNA track is produced at UCSC from mRNA sequence data
submitted to the international public sequence databases by
scientists worldwide.