This perl 5 program forms a averaged graph of GC percentage vs. position along the DNA seq. The program takes as input the DNA seq.

Usage: GC_content [-a -d -i -mX -p# -s# -w#] <DNA.seq >GC.graph.fplot


-a Show AT% instead of the default GC%.

-d Use full degenerate DNA code plus masking character. Default is to consider (a, c, g, t, n) and masking character to be part of the DNA.

-i Interactive input mode.

-mX Change the masking character in the input sequence. The default masking character is 'x'. The masking character is treated as a DNA bp. To specify no masking character, use -m alone, without a following character.

-p# Data points to graph. Default is one per 100 bp.

-s# Fplot shape number for the output, 13 for bars, 14 for blocks. Default is blocks (14).

-q Print out this usage information.

-w# Averaging window size; at each point along the sequence, the GC percentage in a window of # bps will be averaged. Default is 1000 bp.

Example 1: GC_content <DNA.seq >Repeat.graph.fplot

Example 2: GC_content -s9 -w10000 <DNA.seq >Repeat.graph.fplot

Last modified: 5/99

Written by Jim Lund in the lab of Roger Reeves, Johns Hopkins University