GENBLOSUMxx Files

DESCRIPTION:

Program: GENBLOSUMxx-Generation of BLOCK substitution Matrix of least Identity Score xx
Version:version 1
Author:Rifat Nawaz UL Islam, Arnab Nayek, Buddhadev Mondal, Shyamashree Banerjee, 
Parth Sarthi Sen Gupta and Amal Kumar Bandyopadhyay* 
Department of Biotechnology, The University of Burdwan
Interpreter: AWK Programming Language
------------------------
FEATURES:
The program "GENBLOSUMxx" analyze block fasta files of any length and any width and by any name 
>>>>BUT IN .fasta EXTENSION eg block1.fasta, block2.fasta, u_xx_polymerase.fasta, ww-kk-telomerase.fasta etc<<<< 
It can be used for single block or multiple block (whatever present in the current directory).

note: in the example files 7 block fasta files (of length 30 and width 30 are provided)
The program
	a. finds minimum paired identity score for each block 
 	b. compute bit-score in 20x20 format and properties from each block
	c. computes average BLOSUMxx matrix where xx if the average min identity score (see point 1)
	d. list blocks properties and 20x20 bit-score mat in excel table and on the screen


------------------------
INSTRUCTION:

The program run from any UNIX/LINUX/CYGWIN shell
The zip folder "gen-blosum-xx-1.zip" comtains 5 items (APPENDIX 1).
step-by-step 
open shell and 
a. extract files in a directory. 'ls -asl' would show all files. 
b. chmod 600 * (read & write for all); chmod 100 GENBLOSUMxx.exe (execute for prog); check by 'ls -asl'
c. chown owner:group * (eg chown parth:root *); check by 'ls -asl'
d. run the program:  ./GENBLOSUMxx dummy 
-------------------------
IN SUCCESSFUL RUN THE PROG SHOW FOLLOWING DETAILS ON THE SCREEN
----------------------------------------------------------------------------------------------
))))Screen output((((

Program: GENBLOSUMxx-Generation of BLOCK substitution Matrix of least Identity Score xx
	Version:version 1
	Author:Rifat Nawaz UL Islam, Arnab Nayek, Buddhadev Mondal, Shyamashree Banerjee, 
	Parth Sarthi Sen Gupta and Amal Kumar Bandyopadhyay* 
	Department of Biotechnology, The University of Burdwan
	Interpreter: AWK Prog. Lang.
	report bug: akbanerjee[at]biotech[dot]buruniv[dot]ac[dot]in;
	-----------------------------

))))run update((((

  processing    1]  block1.fasta	length   30	 width   30 least identity score 10...
  processing    2]  block2.fasta	length   30	 width   30 least identity score 15...
  processing    3]  block3.fasta	length   30	 width   30 least identity score 14...
  processing    4]  block4.fasta	length   30	 width   30 least identity score 19...
  processing    5]  block5.fasta	length   30	 width   30 least identity score 20...
  processing    6]  block6.fasta	length   30	 width   30 least identity score 14...
  processing    7]  block7.fasta	length   30	 width   30 least identity score 11...
				......done 

))))AVERAGE MATRIX with average score (((( [also in excel format in output file]
			BLOSUM-49: Average Matrix of 7 BLOCKs
    C   S   T   P   A   G   N   D   E   Q   H   R   K   M   I   L   V   F   Y   W
C   4
S   0   6
T   0   0   7
P   0  -1   0   5
A   0  -2  -2  -3   6
G  -3  -3  -4   0  -4   6
N   0   0   0   0  -1  -2   6
D  -1  -2  -1   1  -1  -3   0   5
E   0  -2   0   0  -1  -1   0   0   6
Q   0  -1  -2   0  -3  -3  -1  -2  -1   7
H   1   0   0   0   0   0   3   0   1   1   3
R   0   0   0  -3   0  -2  -1   0  -1   1   0   8
K   0   0  -1  -1   0  -1   0   0   0   0   0   1   7
M   0   0  -2   0  -1  -1   0   0   0  -1   0   0   0   4
I   1  -2   0  -1  -3   0  -1   0   0   0   0  -1  -1   0   6
L   0  -3  -3   0  -4  -2  -1   0  -2  -1   0  -1  -3   1  -2   6
V  -1  -3  -1  -4  -3  -3  -1  -3  -3  -4   0  -2  -1  -2   2  -2   5
F   0  -1   0   0  -2   0   0  -1   0   0   0   0   0   0   0   0  -1   7
Y   0  -3   0   0   0   0   0   0  -1  -1   0  -1  -1   0   0  -2   0   5   5
W   0   0   0   0   0   0   0   0   0   1   0   0  -1   0   0   0   0   1   1   1

))))BLOCK Properties (((( [In excel both absolute and normalized values]
BLOCK properties -Absolute values				
BLAA	BLOCK amino acids;			
HET	Hetero-pairs;			
HOMO	homo-pairs;			
TOT	Total frequency;			
HT_mx	Maximum hetero pair frequency and its type for the given block; 			
HT_mn	Minimum hetero pair frequency and type for the given block;			
Hm_MX	Maximum homo pair frequency and type for the given block;			
HM_MN	minimum homo pair frequency and type for the given block;			


BL	Seqq	WDT	BLAA	HET	HOMO	TOT	HT_mx	Hm_MX		HT_Mn	HM_MN
1	30	30	900	5270	7780	13050	607(IV)	1205(KK)	1(CQ)	1(RR)
2	30	30	900	4180	8870	13050	973(IV)	1795(GG)	1(SP)	1(SS)
3	30	30	900	3278	9772	13050	804(IV)	1823(VV)	1(GH)	1(EE)
4	30	30	900	1908	11142	13050	315(DE)	2033(AA)	1(CS)	1(AA)
5	30	30	900	2397	10653	13050	231(SA)	2428(SS)	1(TF)	1(NN)
6	30	30	900	3306	9744	13050	245(IV)	2060(DD)	1(NW)	1(SS)
7	30	30	900	2289	10761	13050	262(AV)	2278(PP)	1(CS)	1(MM)
			BLOSUM49 and BLOCK properties in >>output_dummy.xls<< file
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Appendix 1 - Files supplied as part of gen-blosum-xx-1.zip 
1) GENBLOSUMxx.exe (APPLICATION) 
2) BLOCK_FASTA FILES : total 7 block fasta files of length 30 and width 30 (act as Input file when present in the run directory) 
3) A dummy (STARTER file) file; if absent in current directory -program autogenerates (no worry).
4) An output of these inputs "output_dummy.xls"
5) Readme (this file) 
END
report bug: akbanerjee[at]biotech[dot]buruniv[dot]ac[dot]in;