This perl 5 script reads the a DNA sequence from the file name given as an argument. The DNA seq. is formatted and sent to the GRAIL server for the indicated service(s). If none of the individual GRAIL searches are selected, program will perform all the GRAIL searches. By default, the DNA is assumed to be of rodent origin.

Usage: grailer [-a -c -d -e[1[a]] -h -i -p -q -r] Dna.seq >Grail.output

Options: -a GRAIL search for polyA sites.

-c GRAIL search for CpG islands.

-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.

-e1a GRAIL search for exons. Default is GRAIL 2 exons, but GRAIL 1 and 1A exons can be selected by -e1 and -e1a, respectively.

-h DNA will be searched for human repetitive elements.

-i Interactive mode. When called this way, the program will ask which options to use, and prompt for a file name.

-p GRAIL search for promoters.

-r DNA will be searched for mouse repetitive elements. This is the default, -r switch not really needed. :) Either -h or -r can be used, but not both.

-q Print out this usage message.

-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.

Last modified: 12/98

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