******************** SGP2 v.1.0. README File ********************

Summary:
A. What's SGP2 ?
B. Installing SGP2
C. File Listing
D. Compiling SGP2
E. To run SGP2
F. Authors and help

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A. What's SGP2 ?
------------------

SGP2 is a program to predict genes by comparing anonymous genomic
sequences from two different species. It combines tblastx, a sequence
similarity search program, with geneid, an "ab initio" gene prediction
program. In "assymetric" mode, genes are predicted in one sequence
from one species (the target sequence), using a set of sequences
(maybe only one) from the other species (the reference set).
Essentially, geneid is used to predict all potential exons along the
target sequence. Scores of exons are computed as log-likelihood
ratios, function of the splice sites defining the exon, the coding
bias in composition of the exon sequence as measured by a Markov Model
of order five, and of the optimal alignment at the amino acid level
between the target exon sequence and the counterpart homologous
sequence in the reference set. From the set of predicted exons, the
gene structure is assembled (eventually multiple genes in both
strands) maximizing the sum of the scores of the assembled exons.

Installation, setup and usage of SGP2 is very easy, and there is a 
range of options to configure output predictions and program behaviour.

SGP2 source code, compiled binaries and documentation are available 
under the GNU GENERAL PUBLIC LICENSE.

Comments and questions are welcome.      

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B. Installing SGP2
--------------------

The SGP2 distribution contains several directories and files. Source 
code and documentation files are included in the distribution.

The distribution is archived and compressed in a single file using the
command tar -zcvf. The compressed file name is SGP2.tar.gz (or something
similar depending on compiled binaries included). The SGP2 files can 
be extracted following these instructions:

Type: 
>tar -zxvf SGP2.tar.gz

After executing these commands, the directory SGP2 will be created 
in your working directory. 

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C. File Listing
---------------

The SGP2 distribution contains the following files and directories:

** bin/
compiled binaries

** docs/
documentation: a short handbook.

** param/
Parameter files.

** samples/
A test sequence and results. 

** src/ 
Source code of SGP2 and parseblast perl programs and source of
genied and blast2gff C programs.

** GNULicense
This software is registered under GNU license.

** Makefile
This file is required to build SGP2 executable files.

** README
This file.

The SGP2 distribution contains a set of independent programs that are
used by SGP2.pl:

* parseblast.pl - a complete parser far any of the blast versions and
outputs.  
* blast2gff     - this program creates non overlapping similarity
regions (SR) from a set of hsp in gff format.
* geneid-sgp    - a modified version of geneid.


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D. Compiling SGP2
-------------------

Move into the SGP2 directory.

Type:
>make 
to compile SGP2.

This will generate the SGP2 executable files within the bin/ subdirectory. 

Type:
>SGP2 -h 

to test the executable file has been correctly created.

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E. To run SGP2
-----------------

There are three environmental variables that can be set by users to their preferences:

   + You must specify the path where SGP2 can find the default files
   with the shell variable "SGP2". 

   + SGP2 needs to write few temporary files in a directory with
   permissions for current user to read and write. Default temporary
   directory path is set to "/tmp/" but you can assign a different
   temporary directory path using the variable "SGP2TMP".

Setting those vars in Bourne-shell and C-shell:

     o Using a Bourne-Shell (e.g. bash):
           export SGP2="path"
           export SGP2TMP="path"

     o Using a C-Shell:
           setenv SGP2 "path"
           setenv SGP2TMP "path"

To run SGP2 type:
>sgp2 [-vhq][-g option] <[-1|-2] fasta_sequence> <-t tblastx_aligment>

For example,
>bin/sgp2  -1 samples/Hsap_BTK.msk.fa  -t samples/Hsap_BTK.tbx 

and to predict genes in the other species,

>bin/sgp2  -2 samples/Mmus_BTK.msk.fa  -t samples/Hsap_BTK.tbx 


TESTING SGP2:

-- The output must contain the same predictions as files 
in samples/Hsap_BTK.sgp2  and samples/Mmus_BTK.sgp2 --

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F. Authors and help
-------------------

SGP2 has been written by Genis Parra, Josep Francesc Abril and Roderic
Guigó (IMIM-UPF-CRG).

SGP2 home page is "http://www1.imim.es/software/SGP2/index.html" and 
SGP2 distributions can be obtained through anonymous ftp to 
"ftp.imim.es" in the directory "/pub/software/SGP2/".

If you need help, send a message to "SGP2@imim.es".