## Description

This track shows the alignments of 32 strains of yeast to the $organism sequence. The sequence for 26 strains of yeast were obtained from downloads.yeastgenome.org/sequence/strains/. An additional six strains were obtained a variety of sequencing centers. Links to all sequences are listed in the following table:

- S. paradoxus - http://www.broad.mit.edu/ftp/pub/annotation/fungi/comp_yeasts/S1a.Assembly/Spar_contigs.fasta
- S. mikatae - http://www-genome.wi.mit.edu/ftp/pub/annotation/fungi/comp_yeasts/S1a.Assembly/Smik_contigs.fasta
- S. kudriavzevii - http://www.genetics.wustl.edu/saccharomycesgenomes/Contigs/YM6553.fsa.gz
- S. bayanus - http://www-genome.wi.mit.edu/ftp/pub/annotation/fungi/comp_yeasts/S1a.Assembly/Sbay_contigs.fasta
- S. castelli - http://www.genetics.wustl.edu/saccharomycesgenomes/Contigs/YM476.fsa.gz
- S. kluyveri - http://www.genetics.wustl.edu/saccharomycesgenomes/Contigs/YM479.fsa.gz
- AWRI1631 - AWRI1631_AWRI_2008_ABSV01000000
- AWRI796 - AWRI796_AWRI_2010_ADVS01000000
- CBS7960 - CBS7960_WashU_2011_AEWL01000000
- CLIB215 - CLIB215_WashU_2010_AEWP01000000
- CLIB324 - CLIB324_WashU_2011_AEWM01000000
- CLIB382 - CLIB382_WashU_2011_AFDG01000000
- EC1118 - EC1118_Genoscope_2009_PRJEA37863
- FL100 - FL100_WashU_2011_AEWO01000000
- FostersB - FostersB_AWRI_2010_AEHH01000000
- FostersO - FostersO_AWRI_2010_AEEZ01000000
- JAY291 - JAY291_Duke_2009_ACFL01000000
- LalvinQA23 - LalvinQA23_AWRI_2011_ADVV01000000
- M22 - M22_WashU_2008_ABPC01000000
- PW5 - PW5_WashU_2011_AFDC01000000
- RM11-1a - RM11-1a_Broad_2005_AAEG01000000
- Sigma1278b - Sigma1278b_MIT_2009_ACVY01000000
- T7 - T7_WashU_2011_AFDE01000000
- T73 - T73_WashU_2011_AFDF01000000
- UC5 - UC5_WashU_2011_AFDD01000000
- Vin13 - Vin13_AWRI_2010_ADXC01000000
- VL3 - VL3_AWRI_2011_AEJS01000000
- W303 - W303_MPG_2011
- Y10 - Y10_WashU_2011_AEWK01000000
- YJM269 - YJM269_WashU_2011_AEWN0100000
- YJM789 - YJM789_Stanford_2007_AAFW02000000
- YPS163 - YPS163_WashU_2008_ABPD01000000

## Methods

Each genome was aligned to the $organism sequence with the lastz aligner from the Penn State Bioinformatics Group. Default parameters for lastz were used. The resulting lav outputs were converted to psl format with the kent source tree program lavToPsl. The psl alignments were chained together with the kent source tree program axtChain with options minimum score of 1000 and the medium linear gap scoring matrix. The chain results were converted to psl format to load into the UCSC genome database.

## Credits

This track was created using the following programs:

- Alignment tools: lastz by Minmei Hou, Scott Schwartz and Webb Miller of the Penn State Bioinformatics Group
- Chaining: axtChain by Jim Kent at UCSC

The data and presentation of these alignments were prepared by Hiram Clawson.

## References

### Chain/Net:

Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9.

### Blastz:

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

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