This directory contains D.pseudoobscura/D.melanogaster alignments made
using the Aug. 2003 D.pseudoobscura assembly (dp1, BCM HGSC Freeze 1) 
vs. the Jan. 2003 D.melanogaster assembly (dm1, BDGP Release 3.1).  

Chained blastz alignments are in chain.gz.  The chain format is 
described here:
    http://www.soe.ucsc.edu/~kent/src/unzipped/hg/mouseStuff/chainFormat.doc

A 'net' file that describes rearrangements between the fruitflies
and the 'best' melanogaster match to any part of pseudoobscura 
is in net.gz.  The net format is described here:
    http://www.soe.ucsc.edu/~kent/src/unzipped/hg/mouseStuff/netFormat.doc


The alignments in axtNet/ are in 'axt' format.   Each alignment contains 
three lines and is separated from the next alignment by a space:   

    Line 1 - summarizes the alignment.   
    Line 2 - contains the D.pseudoobscura sequence with inserts.  
    Line 3 - contains the D.melanogaster sequence with inserts.  

The summary line contains 9 blank separated fields with the 
following meanings:

1 - Alignment number.  The first alignment in a file
    is numbered 0,  the next 1, and so forth.
2 - D.pseudoobscura chromosome.
3 - Start in D.pseudoobscura chromosome.  The first base is
    numbered 1.
4 - End in D.pseudoobscura chromosome.  The end base is included.
5 - D.melanogaster chromosome.
6 - Start in D.melanogaster.
7 - End in D.melanogaster.
8 - D.melanogaster strand.   If this is '-' then the D.melanogaster start/
    D.melanogaster end fields are relative to the reverse complemented
    D.melanogaster chromosome.
9 - Blastz score.   The scoring matrix blastz uses is:

           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 then
    2200 for the second pass, which just restricts
    the search space to the regions between two alignments
    found in the first pass.

The alignments were done with blastz, which is available
from Webb Miller's group at PSU.  Each chromosome
was divided into 10010000 base chunks with 10000 bases
of overlap. The .lav format blastz output, which does not include
the sequence, was converted to .axt with lavToAxt.