This directory contains alignments of the following assemblies:

  - target/reference: Saker falcon
    (falChe1, Feb 2013 (F_cherrug_v1.0/falChe1),
    BGI GCA_000337975.1)

  - query: Peregrine falcon
    (falPer1, Feb 2013 (F_peregrinus_v1.0/falPer1),
    BGI GCA_000337955.1)

Files included in this directory:

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

  - falChe1.falPer1.all.chain.gz: chained blastz alignments. The chain format is
    described in http://genome.ucsc.edu/goldenPath/help/chain.html .

  - falChe1.falPer1.net.gz: "net" file that describes rearrangements between
    the species and the best Peregrine falcon match to any part of the
    Saker falcon genome.  The net format is described in
    http://genome.ucsc.edu/goldenPath/help/net.html .

  - falChe1.falPer1.net.axt.gz: chained and netted alignments,
    i.e. the best chains in the Saker falcon genome, with gaps in the best
    chains filled in by next-best chains where possible.  The axt format is
    described in http://genome.ucsc.edu/goldenPath/help/axt.html .

The falChe1 and falPer1 assemblies were aligned by the blastz alignment
program, which is available from Webb Miller's lab at Penn State
University (http://www.bx.psu.edu/miller_lab/).  Any falChe1 sequences larger
than 20,010,000 bases were split into chunks of 20,010,000 bases overlapping
by 10,000 bases for alignment.  A similar process was followed for falPer1,
with chunks of 10,000,000 overlapping by 0.  Following alignment, the
coordinates of the chunk alignments were corrected by the
blastz-normalizeLav script written by Scott Schwartz of Penn State. 

The blastz scoring matrix (Q parameter) used was:

           A     C     G     T
      A    91  -200  -103  -240
      C  -200   100  -198  -103
      G  -103  -198   100  -200
      T  -240  -103  -200    91

with a gap open penalty of O=400 and a gap extension penalty of E=30.
The minimum score for an alignment to be kept was K=3000 for the first pass
and L=3000 for the second pass, which restricted the search space to the
regions between two alignments found in the first pass.  The minimum
score for alignments to be interpolated between was H=2000.  Other blastz
parameters specifically set for this species pair:
    E=30
    M=50
    O=400
    T=2
    X=810
    Y=3400
    Z=3

The .lav format blastz output was translated to the .psl format with
lavToPsl, then chained by the axtChain program.

Chain minimum score: 3000, and linearGap matrix of (medium):
tableSize   11
smallSize  111
position  1   2   3   11  111 2111  12111 32111  72111 152111  252111
qGap    350 425 450  600  900 2900  22900 57900 117900 217900  317900
tGap    350 425 450  600  900 2900  22900 57900 117900 217900  317900
bothGap 750 825 850 1000 1300 3300  23300 58300 118300 218300  318300

Chained alignments were processed into nets by the chainNet, netSyntenic,
and netClass programs.
Best-chain alignments in axt format were extracted by the netToAxt program.
All programs run after blastz were written by Jim Kent at UCSC.

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If you plan to download a large file or multiple files from this directory,
we recommend you use ftp rather than downloading the files via our website.
To do so, ftp to hgdownload.cse.ucsc.edu, then go to the directory
goldenPath/falChe1/vsFalPer1/. To download multiple files, use the "mget"
command:

    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all files in the current directory)

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

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.

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.