#!/bin/bash PATH=$PATH:/home/january/bin DEBUG="-d" DATE=`date +%d/%m/%Y` DATA=`date +%d/%m/%Y` OLIGODB=oligodb.db VALIDIP="41 14 220 228 231" TITLE="Oligo calculator" if [ $QUERY_STRING ]; then eval `echo $PREFIX$QUERY_STRING | \ sed -e 's/'"'"'/%27/g;s/%2F/\//g;s/+/ /g' | \ awk 'BEGIN{RS="&";FS="="} $1~/^[a-zA-Z][a-zA-Z0-9_]*$/ { printf "%s=%c%s%c\n",$1,39,$2,39}' ` fi cat <Oligo Calculator EOF NAME="unknown" if [ -z "$CONC" ] ; then CONC=50 ; fi if [ -z "$SALT" ] ; then SALT=50 ; fi if [ "$SEQUENCE" ] ; then CONC2=`echo -e "scale=6\n$CONC/1000000" | bc` SALT2=`echo -e "scale=6\n$SALT/1000" | bc` TM=`{ echo "> $NAME" ; echo $SEQUENCE ; } | \ gp_tm -c $SALT2 -M $CONC2` ; LENGTH=`echo -n $SEQUENCE | wc -c` MOLWEIGHT=$[ $LENGTH * 330 ] cat << EOF EOF fi cat <

Oligo calculator

Calculate the Tm, dimere formation and stem /loop structures for an oligonucleotide sequence.

Length = $LENGTH Tm = $TM

Weight = $MOLWEIGHT g/Mol

Dimeres and stem-loop structures found (highest 3 structures):

EOF

	{ echo ">$NAME" ; echo $SEQUENCE ; } | gp_primer -m 3

	cat << EOF

Manual pages:

gp_tm
gp_primer

EOF