MAVG contains a number of C programs for finding CpG islands 
in a genomic sequence


Description file for MAVT program (11/22/2001):

mavg (mavg.c):the main testing program
    Usage: read testing data from the stadard input and output result.
    Important subroutines:
	get_input() [line number 38]
	mln_part() [line number 61]
	mslc() [line number 207]   --> O(n) 

	drs_part() [line number 76]
	mavs() [line number 156]      --> O(n) ?? but analyzed O(nL)?
	Locate() [line number 121] --> used by mavs()
		
	report() [line number 247] --- debug info. to see, turn it on in main()
	clock() ---> builtin function as timer
	NB: 1000 clock = 1 sec.

Input format for mavg.exe:
	n L range seed kk (n integers) 0 0 0 0 0

	Note: n: numbers of elements; L: limit length. 
	      range and seed are output from gen-data for repeated experiment.
	      several sets of tested can be put into one file
	      but must be ended with five zeros: 0 0 0 0 0
	Note: For an example, see [mavg.in] file.
	      currently, the max n allows is 4,000,000 (4 millions), but
	      the number can be changed in source in a machine with larger memeory.
      
Output for mavg.exe:
    First few lines (8) are for debuging purpose, just ignore them
    It follows by two groups of output
    	The first group print the largest averaged [kk] subsequence
    	The second group print the smallest averaged [kk] subsequence
	      

gen-data (gen-data.c): generating random input sequence for mavg.

Input arguments for gen-data.exe:
	Usage: gen-data n L range seed kk
	Note: all these five arguments have default values

Output format for gen-data.exe: Same as the Input format for mavg.exe

First-Time-Tester: (or just run: "sh runme.sh")

	1. Try this: gen-data | mslc -s
	2. Try this: gen-data 3000 | mslc -s
	3. Try this: gen-data 10000 | mslc -s
	4. Try this: gen-data 1000000 | mslc

-- Yaw-Ling Lin, Dept CSIM, PU.

Generation of an input file for MAVT (4/18/2002):

base2no is a program for converting a sequence file in fasta format into
a sequence number of numbers for MAVG. Each dinucleotide is converted into a number.
The usage for base2no is

base2no  Seq  L  K  >  Num_File

where Seq is a file of a DNA sequence in FASTA format,
L >= 10 is the minimum length of regions,
K >= 1 is the number of regions to be reported,
Num_File is an output file of numbers.

Xiaoqiu Huang
Department of Computer Science
Iowa State University
Description file for MAVG program (11/22/2001):