-=- RBS_v1.0 README -=-

Reciprocal BLASTN best-hit search(RBS)is an open source program! More information or 
the latest release please visit the bioinplant homepage:
http://ibi.zju.edu.cn/bioinplant/
====================================================================================

-- DESCRIPTION --

   RBS_v1.0 is a system for rapidly aligning the cds(coding sequence) of chromosome 
A to chromosome B with BLAST program. The current version (release 1.0) can find all 
the paralogus gene pairs for rice genome and reveal the whole genome duplication eve
-nts. The genes are more conserved than  non-coding DNA sequence which is too diverg
-ent to detect similarity.So RBS using coding DNA sequence is an available method to 
study the segmental or whole genome duplication.

-- USAGE --

Usage: $0 -i <chrA_cds_fasta_seq> -I <chrB_cds_fasta_seq> -s <chrA_site> -S <chrB_site> -o <OUTPUT> -b <blast_path>

++++++++++++++++++++++++ RBS Version:1.0 ++++++++++++++++++++++++++++++++

 Options
 -i input chromosome A FASTA cds sequence          [*]     
 -I input chromosome B FASTA cds sequence          [*]
 -s input chromosome A FASTA cds site information  [*]     
 -S input chromosome B FASTA cds site information  [*]
 -o get output file                                [*]
 -b set absolute blast PATH                        [*]
 -g use gnuplot program to plot data,get *.ps file [default: T]
 -d get output data, you can use excel to plot     [default: F]
 -e Blast E-value                                  [default: 1e-14]   
 -x set xlable name for gnuplot                    [default: <chrA_cds_fasta_seq>]
 -y set xlable name for gnuplot                    [default: <chrB_cds_fasta_seq>]

***Attention: parameter [*] means that you must give the specific value 

Example:

Input chromosome fastas cds sequence:
====================================================================================

------------------------------------------------------------------------------------
>9629.m00001#CDS  TBC domain, putative
ATGATTTAGTTTCAAAATATTTTATTTGTAGTACAATACAACTGTACAAAGATGATACATAGACCAATAAATTGATCCATTGTG
ATCCTTAAGCTTAATCAAATAATCCAAAGCCCATATCATCATCTGATTCTGGTTCAGGTTCTTCTTTTTTCTTTTCTTCTTTAG
CTGGTGCACTTTCTGTACTGGCAGGTGCAACTGCTGCTGGTGCTGCTGCTGGTGCTTTTCCAACTCCTGATCCAATATTTGTTA
TAAGTTCTTTTATATTAACTCCTTCTAAAGCTTTAGCAAATAATCCTGGCCAATAAGATTCCACATCAACATTAGCAGCTTTTA
AAATTGTTTGAATTTTTTCTCCAGTTACAGCAACATCGTCATCAACAAGAATTAGTGTTGAATAAACGCAAGCAAGTTCAGCTT
TCTTATTCATGTTTGTCACTTGTATAAAATATATTAAAGCTGGATGGAATGATAAAACGGTGCAAGTCGCTGATATAGCCTTAG
CTCAAGAAAAGNAGAACAAGCACCCGACATTCGCTTGATCCAGCTAAAAGCCTCGTGC  
>9629.m00002#CDS  TBC domain, putative
GCACGAGGTTTTAATTCACAAAAGACGATTTTATTCCTGTTATAAACTTACACTAATTGTCACGTCGAGATTGTTTTCCGCTTC
TTTCATATTTACTACAACTGCTTATTATATCGTCTACATATATATCAAGATTTCGAATAATTTTATAAATGAATCTTCAATGAT
GATTCTCAATTTATTGAATTAAACATTAATGCCGAGCTTCTTCGCTTCTTCCTCGAATTTGACTCTGTACTTCTTGTCTGGGTC
GTATTTGTTGGCAAGGGAATCCCACAATTCTGGCTTATTCTCGACCAAGAACTTGATCACTTTCTTGATCACCTCTCGTTGCTT
CTCAGAGCATTTTTTGCAATCGGTGGCCAGAGCATCAGGCAAGACTCGTTTAAGTTCATTTCCTTCTGCTGTGCATCTTCCTTC
ATCCATCAAACACTTGAAGTAATTGTTCAACAAACGTTCACTATGCAGAATTTCATCCACATTAATATTGTCAAATTTAGATGT
ATATGAAGATTCCCTCGTGC
..............
------------------------------------------------------------------------------------

*****Attention: 
1)you must give Multi-FASTA format. follow the ">",you shoud give the
specific cds accession number or model_name,which corresponding the site file.
Also you MUST ADD "#" to distinguish the discription of the cds function.
2)The default search use blastn program, if you use the protein sequences to serach,
you must change RBS_v1.0.pl 74~80 lines. change the code as:
        a)formatdb -p value change F into T
        b)blastall -p value change blastn into blastp
         
====================================================================================

Input chromosome cds site information:
<This File descript the cds location in the chromosome>

------------------------------------------------------------------------------------
model_name	end5	end3
9629.m00001	1	7364
9629.m00002	1	7364
9629.m00003	9046	8174
9629.m00004	9523	12619
.....
------------------------------------------------------------------------------------
====================================================================================

Output file:

The result of plot data using gnuplot program,and the graphic file is output.ps

====================================================================================
Parameter:

-b blast executable file path, set such as "-b /usr/bin/blast".

-g default value is "T", if using gnuplot program to plot data, need not set -g value. 

-d default value is "F",output:XXX.exl && XXX_Rev.exl(reverse),you can plot with excel.

-e default value is "1e-14",you can set Blast E-value with different value.                                 

-x default value is <chrA_cds_fasta_seq>,set xlable name for gnuplot.     

-y default value is <chrB_cds_fasta_seq>,set ylable name for gnuplot.                    

====================================================================================

-- CONTACT INFORMATION --

Reference
====================================================================================
ZHANG Yang, et al. Journal of Zhejiang University SCIENCE, 2005 6B(2): 87-90
  
Please address questions and bug reports to: <bioinplant@zju.edu.cn>
Author: Xingyi Guo
Last Revised April 14, 2003
