Program Name: RAPSearch (rapsearch)
Version: 2.22 -- *** a version that supports multiple threads **
Released: Oct 27, 2014 (RAPSearch2.0 was released May 26, 2011)
Developers: Yongan Zhao <yongzhao@indiana.edu> Yuzhen Ye <yye@indiana.edu>, and Haixu Tang <hatang@indiana.edu>
Affiliation: School of Informatics and Computing, Indiana University, Bloomington

The development of rapsearch was supported by NIH grant 1R01HG004908 to YY

rapsearch is free software under the terms of the GNU General Public License as published by 
the Free Software Foundation.

>> If you are switching from RAPSearch1.0 to RAPSearch2.0
   RAPSearch2 runs faster than RAPSearch1, uses less memory,
   and best of all, RAPSearch2 supports mult-threads!!
   You can define the number of threads that you want to use by setting -z parameter (see below)

   NOTE: if you switch from RAPSearch1.0 to RAPSearch2.0, 
	you need to re-run prerapsearch to prepare new database files!!

>> Before you start
   RAPSearch means Reduced Alphabet based Protein similarity Search 

   A linux/unix computer that has 4G memory should be sufficient 
   for similarity search against database of any size

   RAPSearch2 on the web: 
   http://rapsearch2.sourceforge.net/
   http://omics.informatics.indiana.edu/mg/RAPSearch2
  (please check the project home page for updates and newer version of the rapsearch)
   (RAPSearch1 on the web: http://omics.informatics.indiana.edu/mg/RAPSearch)

>> Installation

   simply call: ./install

   The executable files "rapsearch" and "prerapsearch"
   rapsearch:    the similarity search tool
   prerapsearch: the program that generates similarity search database files to be used by rapsearch

   Install RAPSearch2 on Mac OS X:
   #3
   
>> Using prerapsearch & rapsearch

 1.Before using rapsearch for similarity search against a database, 
   run prerapsearch to prepare similarity search database files

   Note: if you switch from RAPSearch1.0 to RAPSearch2.0, you need to re-run prerapsearch to prepare new database files!!

   Usage: prerapsearch -d database(FASTA file) -n processed-db-file

   Example 1: prerapsearch -d nogCOGdomN95.seq -n nogCOGdomN95_db
   Input: nogCOGdomN95.seq (a fasta file)
   Outputs: nogCOGdomN95_db (a binary file) & a couple of other files

   Example 2: prerapsearch -d nr_fasta -n nr_db
   Input: nr_fasta (NCBI nr file in FASTA format)
   Outputs: nr_db

 2.Using rapsearch for similarity search

   Usage: type rapsearch for usages

   Example 1: rapsearch -q 4440037.3.dna.fa -d nogCOGdomN95_db -o 4440037.3.dna-vs-nogCOGdomN95 -z 4
   Input:  4440037.3.dna.fa #query file, note if it is a file of short nucleotide sequences, 
    	   nogCOGdomN95_db     #the base name of the similarity search database 
   (here -z is set to 4, so that four threads be used) 

   Output: 4440037.3.dna-vs-nogCOGdomN95.m8  #the similarty search result, 
                                             #one hit in one line, like -m 8 output from blast
					     #note the only difference is that log10(E-value) is listed in the file
  		  			     #maximum 500 hits per query
   Output: 4440037.3.dna-vs-nogCOGdomN95.aln #detailed alignments
					     #maximum 100 alignments per query

   Example 2: cat 4440037.4440037.3.dna | rapsearch -q stdin -d nogCOGdomN95_db -o 4440037.3.dna-vs-nogCOGdomN95 -z 4
   Input: stdin of system. 
   It's easy and convinient to incorporate RAPSearch into the pipeline

   Example 3: rapsearch -q 4440037.3.dna.fa -d nogCOGdomN95_db -o 4440037.3.dna-vs-nogCOGdomN95 -z 4 -b 0
   Output: Only output m8 file.

   Example 4: rapsearch -q 4440037.3.dna.fa -d nogCOGdomN95_db -z 4 -u 1
   Output: Only generate m8 file and output it to stdout of system.
   It's easy and convinient to incorporate RAPSearch into the pipeline

   Notes:  
 	  a) By default, rapsearch program uses only one thread; you may use -z to change the threads
	  b) RAPSearch outputs hits with log_10(E-value) < 1 (i.e., E-value of 10);
             you may change this by setting log_10(E-value) using -e option
	  c) You may also try -v and -b options to change the number of database sequences that you want to output.

>> More notes 
   1. The sample files (e.g.,4440037.3.dna.fa & nogCOGdomN95.seq) are available at the rapsearch website; nr can
   be downloaded from NCBI ftp site. 
   2. For big similarity search database (like nr), prerapsearch automatically splits the database into 
   several files to reduce the memory requirement. If you need further reduce the memory usage,
   you can choose to use -s option to run prerapsearch