*** INSTALLATION ***

At the unix prompt type:

tar zxvf blast2ps.tar.gz

This will create:

blast2ps/
blast2ps/examples/
blast2ps/examples/example.ps
blast2ps/examples/example.pdf
blast2ps/examples/example.gif
blast2ps/RELEASE
blast2ps/README
blast2ps/blast2ps
blast2ps/CHANGELOG

You can run blast2ps from this directory or put it whereever you want. 
A good place might be /usr/local/bin or some location in your PATH
variable.

If someone gets this to run in a non unix environment I'd like to hear
about it. I haven't tried to run it on Windows or Mac.

*** HOW TO USE ***

You will need a blast output file that can be parsed by BPlite.pm.  I
try to keep BPlite.pm updated to deal with parsing errors as they
arise so please notify me if you have blast output that can't be
parsed.

To run type:

blast2ps <blast-output-path-name> <expectation-cutoff> > file-name.ps

See below for explanation of <expectation-cutoff>

You should be able to view the output with gv or some other postscript
viewer and/or print it to a postscript printer.


*** OUTPUT FORMAT ***

If the first HSP of a database hit has an expectation value less than
or equal to <expectation-cutoff> all the HSPs in the blast output for
this database sequences are represented relative to where they match
the query sequence.

All HSPs for a database hit are displayed on the same line.  The
height of the line is proportional to the percent identity by the
following relationship:

HSP_HEIGHT = MAX_LINE_HEIGHT * exp((PERCENT_ID - 100) / 20)

The HSPs are colored as in the NCBI graphical output by bit scores.

*** PROBLEMS, QUESTIONS, SUGGESTIONS ***

email: dwrice@indiana.edu
