Description
This track displays translated blat alignments of expressed sequence tags
(ESTs) in GenBank from organisms other than human.
ESTs are single-read sequences, typically about 500 bases in length, that
usually represent fragments of transcribed genes.
Display Conventions and Configuration
This track follows the display conventions for
PSL alignment tracks. In dense display mode, the items that
are more darkly shaded indicate matches of better quality.
The strand information (+/-) for this track is in two parts. The
first + or - indicates the orientation of the query sequence whose
translated protein produced the match. The second + or - indicates the
orientation of the matching translated genomic sequence. Because the two
orientations of a DNA sequence give different predicted protein sequences,
there are four combinations. ++ is not the same as --, nor is +- the same
as -+.
The description page for this track has a filter that can be used to change
the display mode, alter the color, and include/exclude a subset of items
within the track. This may be helpful when many items are shown in the track
display, especially when only some are relevant to the current task.
To use the filter:
- Type a term in one or more of the text boxes to filter the EST
display. For example, to apply the filter to all ESTs expressed in a specific
organ, type the name of the organ in the tissue box. To view the list of
valid terms for each text box, consult the table in the Table Browser that
corresponds to the factor on which you wish to filter. For example, the
"tissue" table contains all the types of tissues that can be
entered into the tissue text box. Multiple terms may be entered at once,
separated by a space. Wildcards may also be used in the
filter.
- If filtering on more than one value, choose the desired combination
logic. If "and" is selected, only ESTs that match all filter
criteria will be highlighted. If "or" is selected, ESTs that
match any one of the filter criteria will be highlighted.
- Choose the color or display characteristic that should be used to
highlight or include/exclude the filtered items. If "exclude" is
chosen, the browser will not display ESTs that match the filter criteria.
If "include" is selected, the browser will display only those
ESTs that match the filter criteria.
This track may also be configured to display base labeling, a feature that
allows the user to display all bases in the aligning sequence or only those
that differ from the genomic sequence. For more information about this option,
go to the
Base Coloring for Alignment Tracks page.
Several types of alignment gap may also be colored;
for more information, go to the
Alignment Insertion/Deletion Display Options page.
Methods
To generate this track, the ESTs were aligned against the genome using
blat. When a single EST aligned in multiple places, the
alignment having the highest base identity was found. Only alignments
having a base identity level within 0.5% of the best and at least 96% base
identity with the genomic sequence were kept.
Credits
This track was produced at UCSC from EST sequence data submitted to the
international public sequence databases by scientists worldwide.
References
Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW.
GenBank.
Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42.
PMID: 23193287; PMC: PMC3531190
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL.
GenBank: update.
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6.
PMID: 14681350; PMC: PMC308779
Kent WJ.
BLAT - the BLAST-like alignment tool.
Genome Res. 2002 Apr;12(4):656-64.
PMID: 11932250; PMC: PMC187518
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