This directory contains human/chimpanzee "reciprocal best" alignments 
made using the Jul. 2003 human assembly (NCBI Build 34, UCSC hg16)
and the 13 Nov. 2003 Arachne 4x draft chimp assembly from
the Broad Institute, MIT/Harvard, with sequence provided by
the Broad Institute and Washington University, St. Louis.
The Chimpanzee Genome Sequencing project was sponsored by
NHGRI.

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 chimp 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 - Human chromosome.
3 - Start in human chromosome. The first base is
    numbered 1.
4 - End in human chromosome. The end base is included.
5 - Chimp scaffold.
6 - Start in chimp scaffold.
7 - End in chimp scaffold.
8 - Chimp strand. If this is '-', the chimp start/end fields are 
    relative to the reverse-complemented chimp scaffold.
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 Pennsylvania State University (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 PSU's lavToAxt.

The axtBest subset covers 40% of the human genome. 


      Name                    Last modified      Size  Description
Parent Directory - chr1.axt.gz 2003-12-19 13:37 87M chr10.axt.gz 2003-12-19 13:37 52M chr10_random.axt.gz 2003-12-19 13:37 180K chr11.axt.gz 2003-12-19 13:38 52M chr12.axt.gz 2003-12-19 13:38 51M chr13.axt.gz 2003-12-19 13:38 39M chr13_random.axt.gz 2003-12-19 13:38 4.1K chr14.axt.gz 2003-12-19 13:38 35M chr15.axt.gz 2003-12-19 13:38 32M chr15_random.axt.gz 2003-12-19 13:38 40K chr16.axt.gz 2003-12-19 13:38 30M chr17.axt.gz 2003-12-19 13:39 29M chr17_random.axt.gz 2003-12-19 13:39 146K chr18.axt.gz 2003-12-19 13:39 31M chr18_random.axt.gz 2003-12-19 13:39 685 chr1_random.axt.gz 2003-12-19 13:39 259K chr19.axt.gz 2003-12-19 13:39 19M chr19_random.axt.gz 2003-12-19 13:39 5.6K chr2.axt.gz 2003-12-19 13:39 96M chr20.axt.gz 2003-12-19 13:39 24M chr21.axt.gz 2003-12-19 13:40 13M chr22.axt.gz 2003-12-19 13:40 12M chr2_random.axt.gz 2003-12-19 13:40 48K chr3.axt.gz 2003-12-19 13:40 80M chr3_random.axt.gz 2003-12-19 13:40 4.2K chr4.axt.gz 2003-12-19 13:40 76M chr4_random.axt.gz 2003-12-19 13:40 41K chr5.axt.gz 2003-12-19 13:41 72M chr5_random.axt.gz 2003-12-19 13:41 356 chr6.axt.gz 2003-12-19 13:41 68M chr6_random.axt.gz 2003-12-19 13:41 131K chr7.axt.gz 2003-12-19 13:41 60M chr7_random.axt.gz 2003-12-19 13:41 70K chr8.axt.gz 2003-12-19 13:41 58M chr8_random.axt.gz 2003-12-19 13:41 81K chr9.axt.gz 2003-12-19 13:42 45M chr9_random.axt.gz 2003-12-19 13:42 261K chrM.axt.gz 2003-12-19 13:42 3.8K chrUn_random.axt.gz 2003-12-19 13:42 519K chrX.axt.gz 2003-12-19 13:42 38M chrX_random.axt.gz 2003-12-19 13:42 117K chrY.axt.gz 2003-12-19 13:42 3.9M md5sum.txt 2003-12-19 19:20 2.0K