This directory contains alignments of the following assemblies:

  - target/reference: Human (hg18, Mar. 2006, NCBI Build 36.1)

  - query: Cow (bosTau3, August 2006, Baylor Release 3.1)

Files included in this directory:

  - md5sum.txt: md5sum checksums for the files in this directory

  - hg18.bosTau3.syn.net.gz: "syntenic net" file.  This is the net 
    filtered to remove non-syntenic alignments

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To download a large file or multiple files from this directory, we recommend 
that you use ftp rather than downloading the files via our website. To do so: 
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/hg18/vsBosTau3

To download multiple files from the UNIX command line, use the "mget" command. 
    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all the files in the directory) 
Use the "prompt" command to toggle the interactive mode if you do not want 
to be prompted for each file that you download.

All files in this directory are freely available for public use.

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References

Harris, R.S. (2007) Improved pairwise alignment of genomic DNA
Ph.D. Thesis, The Pennsylvania State University

Chiaromonte, F., Yap, V.B., and Miller, W.  Scoring pairwise genomic
sequence alignments.  Pac Symp Biocomput 2002, 115-26 (2002).

Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.
Evolution's cauldron: Duplication, deletion, and rearrangement in the
mouse and human genomes. Proc Natl Acad Sci USA 100(20), 11484-11489
(2003).

Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.,
Haussler, D., and Miller, W.  Human-mouse alignments with BLASTZ</A>.
Genome Res. 13(1), 103-7 (2003).