This directory contains the Feb. 2008 assembly of the guinea pig genome
(cavPor3, Broad Institute cavPor3), as well as repeat annotations and GenBank sequences.

This assembly was produced by the Broad Institute at MIT and Harvard.
For more information on the guinea pig genome, see the project website:
  http://www.broad.mit.edu/mammals/
  
Files included in this directory:

cavPor3.2bit - contains the complete guinea pig/cavPor3 genome sequence
    in the 2bit file format.  Repeats from RepeatMasker and Tandem Repeats
    Finder (with period of 12 or less) are shown in lower case; non-repeating
    sequence is shown in upper case.  The utility program, twoBitToFa (available
    from the kent src tree), can be used to extract .fa file(s) from
    this file.  A pre-compiled version of the command line tool can be
    found at:
        http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
    See also:
        http://genome.ucsc.edu/admin/git.html
	http://genome.ucsc.edu/admin/jk-install.html

cavPor3.agp.gz - Description of how the assembly was generated from
    fragments.

cavPor3.fa.gz - "Soft-masked" assembly sequence in one file.
    Repeats from RepeatMasker and Tandem Repeats Finder (with period
    of 12 or less) are shown in lower case; non-repeating sequence is
    shown in upper case.

cavPor3.fa.masked.gz - "Hard-masked" assembly sequence in one file.
    Repeats are masked by capital Ns; non-repeating sequence is shown in
    upper case.

cavPor3.fa.out.gz - RepeatMasker .out file.  RepeatMasker was run with the
    -s (sensitive) setting.
    #    Jan 11 2008 (open-3-1-9) version of RepeatMasker
    #    CC   RELEASE 20071204;

cavPor3.trf.bed.gz - Tandem Repeats Finder locations, filtered to keep repeats
    with period less than or equal to 12, and translated into UCSC's BED
    format.

est.fa.gz - Guinea Pig ESTs in GenBank. This sequence data is updated once a
    week via automatic GenBank updates.

cavPor3.quals.fa.gz - quality scores in fasta file format

md5sum.txt - checksums of files in this directory

mrna.fa.gz - Guinea Pig mRNA from GenBank. This sequence data is updated
    once a week via automatic GenBank updates.

upstream1000.fa.gz - Sequences 1000 bases upstream of annotated
    transcription starts for Xeno RefSeq genes with annotated 5' UTRs.  
    This file is updated weekly so it could be slightly out
    of sync with the Xeno RefSeq data which is updated daily for most 
    assemblies.

upstream2000.fa.gz - Same as upstream1000, but 2000 bases.

upstream5000.fa.gz - Same as upstream1000, but 5000 bases.

xenoMrna.fa.gz - GenBank mRNAs from species other than that of 
    the genome. This sequence data is updated once a week via automatic 
    GenBank updates.

cavPor3.chrom.sizes - Two-column tab-separated text file containing assembly
    sequence names and sizes.

cavPor3.chromAlias.txt - sequence name alias file, one line
    for each sequence name.  First column is sequence name followed by
    tab separated alias names.

------------------------------------------------------------------
If you plan to download a large file or multiple files from this
directory, we recommend that you use ftp rather than downloading the
files via our website. To do so, ftp to hgdownload.cse.ucsc.edu
[username: anonymous, password: your email address], then cd to the
directory goldenPath/cavPor3/bigZips. To download multiple files, use
the "mget" command:

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

Alternate methods to ftp access.

Using an rsync command to download the entire directory:
    rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/cavPor3/bigZips/ .
For a single file, e.g. chromFa.tar.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/cavPor3/bigZips/chromFa.tar.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/cavPor3/bigZips/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/cavPor3/bigZips/chromFa.tar.gz' 
        -O chromFa.tar.gz

To unpack the *.tar.gz files:
    tar xvzf <file>.tar.gz
To uncompress the fa.gz files:
    gunzip <file>.fa.gz

The Guinea Pig sequence is made freely available before scientific publication 
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 if the provider of these data (The Broad Institute) is 
      properly acknowledged.
   3. The center producing the data reserves the right to publish the initial 
      large-scale analyses of the data set, including large-scale identification 
      of regions of evolutionary conservation and large-scale genomic assembly. 
      Large-scale refers to regions with size on the order of a chromosome (that 
      is, 30 Mb or more).
   4. Any redistribution of the data should carry this notice. 1. The data may 
      be freely downloaded, used in analyses, and repackaged in databases.