This directory contains alignments of the D. melanogaster assembly 
(dm1, Jan. 2003, BDGP Release 3) to the D. virilis assembly (droVir1, 
Agencourt 12 July 2004).

Files included in this directory:

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

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

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

  - melanogasterNet.gz: contains chained and netted alignments, i.e. the
    best chains in the genome, with gaps in the best chains filled in 
    by next-best chains where possible. 

The alignments in melanogasterNet are in "axt" format. For a description, 
see http://genome.ucsc.edu/goldenPath/help/axt.html.

The alignments were produced by the blastz alignment program, which 
is available from Webb Miller's lab at Penn State University 
(http://www.bx.psu.edu/miller_lab/). The blastz scoring matrix used was:

           A    C    G    T
      A   91 -114  -31 -123
      C -114  100 -125  -31
      G  -31 -125  100 -114
      T -123  -31 -114   91

with a gap open penalty of 400 and a gap extension penalty of 30.  The 
minimum score for an alignment to be kept was 3000 for the first pass  
and 2200 for the second pass, which restricted the search space to the 
regions between two alignments found in the first pass.

Each chromosome was divided into 10,000,000 base chunks with 10000 bases
of overlap. The .lav format blastz output, which does not include
the sequence, was converted to .axt with lavToAxt. 

The axtNet alignments were processed with chainNet, netSyntenic,
and netClass written by Jim Kent at UCSC.

----------------------------------------------------------------
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/droVir1/vsDm1/. To download multiple 
files, use the "mget" command:

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

The D. virilis data have been freely provided by Agencourt Bioscience 
Corporation before publication for use in the UCSC Genome Browser with the 
following understanding: 

1. The data may be freely downloaded, used in analyses, and repackaged in
   databases. 

2. Users are free to use the data in scientific papers analyzing particular 
   genes and regions, provided that the Agencourt is properly acknowledged. 

3. Agencourt reserves the right to publish the initial large-scale analyses 
   of the dataset, including large-scale identification of regions of 
   evolutionary conservation and large-scale genomic assembly. 

4. Any redistribution of the data should carry this notice. 


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