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:

  1. 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.
  2. 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.
  3. 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.