Description
This track shows the level of agreement between the multiple sequence alignments
in ENCODE regions generated by the programs MAVID, MLAGAN, and TBA (v2).
The alignments were taken from the Sep. 2005 ENCODE MSA freeze.
Each subtrack in the annotation shows the base-by-base agreement
between alignments generated by two of the three programs. An additional
subtrack shows the overall mean agreement among all three alignment pairs.
Display Conventions and Configuration
This annotation follows the display conventions for composite
tracks. The subtracks within this annotation
may be configured in a variety of ways to highlight different aspects of the
displayed data. The graphical configuration options are shown at the top of
the track description page, followed by a list of subtracks. To display only
selected subtracks, uncheck the boxes next to the tracks you wish to hide.
For more information about the graphical configuration options, click the
Graph
configuration help link.
Methods
The agreement for a given human base was computed as the fraction of species
other than human in which the alignments from the two programs exactly agree.
Two alignments can agree by aligning the human to the same base in
another species or by both aligning the human base to a gap in the other
species.
Note that when two programs both align a human base to gaps in all other
species, there is perfect agreement. This is somewhat misleading,
because the agreement in the alignment may be simply an artifact of missing
sequence in the other species. To facilitate analysis in these instances,
the MSA Alignment Gaps (Align Gap) annotation track has been provided to show
the number of ungapped species for every base in every alignment.
Credits
The agreement tracks were generated by
Lior Pachter
and Ariel
Schwartz of UC Berkeley.
References
Schwartz AS, Myers EW, Pachter L.
Alignment metric
accuracy. Submitted. 2007.
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