Read Me

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####### The Analysis and Annotation Tool (AAT) Package ########
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Developed by Xiaoqiu Huang, described in:

A Tool for Analyzing and Annotating Genomic Sequences, Genomics 46,37-45 (1997)


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Building the tools.

The AAT package includes the following tools:

        dds (a blast-like dna/dna search and alignment tool)
        gap2 (nucleotide spliced alignment tool)

        dps (a blast-linke protein/dna search and alignment tool)
        nap (protein to genome spliced alignment tool)

        ext and filter (output parsing tools required by the above)

        show (multiple alignment tool, given gap2 and nap outputs)




To recompile the source code, type:

    ./configure --prefix=`pwd`

    make

    make install



The executables will be placed in the /bin directory.  




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The cDNA/EST alignment pipeline includes:

dds -> ext -> filter -> gap2

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The protein spliced alignment pipeline includes:
dps -> ext -> filter -> nap

The resulting gap2 and nap output files for a single genomic DNA sequence query can be combined into a multiple alignment (very useful visualization tool) using show.

ie.  
show *gap2 *nap > mult_alignment_file.txt


#### AAT.pl Perl script used to facilitate running the pipeline:

The AAT.pl script is used to provide a single interface to running the entire AAT pipeline. 


## Sample data and pipeline execution ##

See the sample_data/ contents, and try running the 'runMe.sh' script, which provides an example of how to execute the software.



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Release notes:
release-08-16-2005:  dps modified by Xiaoqiu Huang to use a mega-chain hsp-chaining algorithm.   This yields improved alignments via the dps/nap pipeline, especially in regions with tandem gene duplicates.


release-03-05-2011:  first release as open source on sourceforge