This directory contain chimpanzee/human alignments made
using the Nov 2003 Arachne chimp assembly 
(NCBI Build 1 Version 1, UCSC panTro1)
vs. the Human July 2003 human assembly
(NCBI Human Build 34, UCSC hg16). 

The axtNet directory contains alignments indicating the best chimp/human chain for
every part of the human genome. For more information on the algorithms used
to generate these alignments, see the Methods section of the
Human Chain and Human Net tracks in the chimpanzee browser.

The alignments 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 human sequence with inserts.  
    Line 3 - contains the mouse 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 - Target (chimpanzee) chromosome.
3 - Start in target (chimp) chromosome. The first base is
    numbered 1.
4 - End in target (chimp) chromosome. The end base is included.
5 - Query (human) chromosome.
6 - Start in query (human).
7 - End in query (human).
8 - Query (human) strand. If this is '-', the query start/end fields are 
    relative to the reverse-complemented query chromosome.
9 -  score.