## 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.