APBEST Files

README
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Program: APBEST--Analysis of Protein Block and Evaluation of Substitution Type										
Version:--v01:10B										
Author:(c)--Parth Sarthi Sen Gupta, Shyamashree Banerjee, Chittran Roy,Rifat Nawaz Ul Islam, Buddhadev Mondal, 
Arnab Nayek and Amal Kumar Bandyopadhyay*; 								
Department of Biotechnology, The University of Burdwan, WB, India, 713104														
Program--interpretated by AWK (1986): (P Rubin, J. Fenlason, Ridhard Stallman and A. D. Robbins)										
report bug: akbanerjee[at]biotech[dot]buruniv[dot]ac[dot]in;

ARTICLE: Parth Sarthi Sen Gupta, Shyamashree Banerjee, Chittran Roy,Rifat Nawaz Ul Islam, Buddhadev Mondal, Arnab Nayek and Amal Kumar Bandyopadhyay*, 
"Automated Approach for Understanding Molecular Evolution of Homologous Proteins" (submitted)										

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The program can be executed either from UNIX/LINUX or WINDOW command prompt which takes BLOCK fasta file
 (Appendix 1: file 2) as input and redirect output in an excel format (Appendix 1: File 3).

INSTRUCTIONs:
If you are reading this means you are already downloaded the APBEST and its corresponding files:
  A] run from windor command prompt--
	1. window should have gawk/awk binary;; can be downloaded from following link or elsewhere
	   http://gnuwin32.sourceforge.net/packages/gawk.htm
	2. unzip in a proper location eg C:\AWK
	3. include the bin directory in window-path  variable: (->==click; ->>right click)
        *->start->>computer->properties->Advance system settings->environment variables->user variable-<new>
	[Note: if path not exist then type <new>; if it does just click edit highlighting path]
	4. variable name-- path 
	   variable value-- C:\AWK\bin
	5. click ok
	6. open a command prompt
	7. type awk
	   it will print many things
	   if it does then it is done else repeat the above steps (1 to 7) correctly.
	8. Now in a command prompt type APBEST block_fasta_input_file (provided as ldh_m-bl._inline._BLOCK.fasta)
        9. locate output (name ldh_m-bl._inline._BLOCK.xls in the present directory and also provided in the OUTPUT folder)
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  B] for execution of APBEST in UNIX/LINUX SHELL:
        1. Put the APBEST in a directory in your drive, do chmod (executable) and chown (ownership) if needed.
        2. In that directory type ./APBEST block_fasta_input_file
        3. as step 9 (see above)
[note: alternatively the program can be kept in some system or user specific bin dir whose path to be included 
in .login etc file. in this case program can be called from any dir] 
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Appendix 1 -  Files supplied as part of APBEST

1) APBEST.exe (APPLICATION)
2) Example block_fasta_file.fasta (Input file) 
3) Example output_file.xls (OUTPUT-folder)
4) Readme (this file)

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