## Description

This track displays human-centric multiple sequence alignments in the ENCODE regions for the 28 vertebrates included in the September 2005 ENCODE MSA freeze, based on comparative sequence data generated for the ENCODE project as well as whole-genome assemblies residing at UCSC, as listed:

- human (May 2004, hg17)
- armadillo (NISC and May 2005 Broad Assisted Assembly v 1.0)
- baboon (NISC)
- chicken (Feb 2004, galGal2)
- chimp (Nov 2003, panTro1)
- colobus_monkey (NISC)
- cow (BCM)
- dog (July 2004, canFam1)
- dusky_titi (NISC)
- elephant (NISC and May 2005 Broad Assisted Assembly v 1.0)
- fugu (Aug 2002, fr1)
- galago (NISC)
- hedgehog (NISC)
- macaque (Jan 2005, rheMac1)
- marmoset (NISC)
- monodelphis (Oct 2004, monDom1)
- mouse (Mar 2005, mm6)
- mouse_lemur (NISC)
- owl_monkey (NISC)
- platypus (NISC and Aug 2005 Mullikin Phusion Assembly of WUGSC Traces)
- rabbit (NISC and May 2005 Broad Assisted Assembly v 1.0)
- rat (June 2003, rn3)
- rfbat (NISC)
- shrew (NISC and Sep 2005 Mullikin Phusion Assembly of Broad Traces)
- tenrec (Apr 2005 Mullikin Phusion Assembly of Broad Traces)
- tetraodon (Feb 2004, tetNig1)
- xenopus (Oct 2004, xenTro1)
- zebrafish (June 2004, danRer2)

The alignments in this track were generated using the Threaded Blockset Aligner (TBA). The Genome Browser companion tracks, TBA Cons and TBA Elements, display conservation scoring and conserved elements for these alignments based on various conservation methods.

## Display Conventions and Configuration

In full display mode, this track shows pairwise alignments of each species aligned to the human genome. In dense mode, the alignments are depicted using a gray-scale density gradient. The checkboxes in the track configuration section allow the exclusion of species from the pairwise display.

When zoomed-in to the base-display level, the track shows the base composition of each alignment. The numbers and symbols on the "Gaps" line indicate the lengths of gaps in the human sequence at those alignment positions relative to the longest non-human sequence. If there is sufficient space in the display, the size of the gap is shown; if not, and if the gap size is a multiple of 3, a "*" is displayed, otherwise "+" is shown. To view detailed information about the alignments at a specific position, zoom in the display to 30,000 or fewer bases, then click on the alignment.

## Methods

The TBA was used to align sequences in the September 2005 ENCODE sequence data freeze. Multiple alignments were seeded from a series of combinatorial pairwise blastz alignments (not referenced to any one species). The specific combinations were determined by the species guide tree. The resulting multiple alignments were projected onto the human reference sequence.

## Credits

The TBA multiple alignments were created by Elliott Margulies of NHGRI, while at the Green Lab.

The programs Blastz and TBA, which were used to generate the alignments, were provided by Minmei Hou, Scott Schwartz and Webb Miller of the Penn State Bioinformatics Group.

The phylogenetic tree is based on Murphy et al. (2001).

## References

Blanchette M, Kent WJ, Reimer C, Elnitski L, Smit A, Roskin K, Baertsch R, Rosenbloom KR, Clawson H et al. Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner. Genome Res. 2004;14(4):708-15.

Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002;115-26.

Murphy WJ, Eizirik E, O'Brien SJ, Madsen O, Scally M, Douady CJ, Teeling E, Ryder OA, Stanhope MJ, de Jong WW et al. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science. 2001;294(5550):2348-51.

Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison R, Haussler D, Miller W. Human-Mouse Alignments with BLASTZ. Genome Res. 2003;13(1):103-7.