$wordfile
SSN3 CDK8 GIG2 NUT7 RYE5 SRB10 UME5
.
.

$textfile
17170106|Perturbation of the activity of replication origin by meiosis
+ specific transcription.|We have determined the activity of all ARSs 
+on the Saccharomyces cerevisiae chromosome VI as chromosomal replicat
+ion origins in pre-meiotic S-phase by neutral/neutral 2D gel-electrop
+horesis. The comparison of origin activity of each origin in mitotic 
+and pre-meiotic S-phase showed that one of the most efficient origins
+ in mitotic S-phase, ARS605, was completely inhibited in pre-meiotic 
+S-phase. ARS605 is located within the ORF of Msh4 gene that is transc
+ribed specifically during an early stage of meiosis. Systematic analy
+ses of relationships between Msh4 transcription and ARS605 origin act
+ivity revealed that transcription of Msh4 inhibited the ARS605 origin
+ activity by removing ORC from ARS605. Deletion of UME6 {{UME6}}, a t
+ranscription factor responsible for repressing Msh4 during mitotic S-
+phase, resulted in inactivation of ARS605 in mitosis. Our finding is 
+the first demonstration that the transcriptional regulation on the re
+plication origin activity is related to changes in cell physiology. T
+hese results may provide insights into changes in replication origin 
+activity in embryonic cell cycle during early developmental stages.
.
.
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#!/usr/bin/perl
use warnings;
use strict;


if ($#ARGV != 4) {
 print "usage: run batch file 'run' not this one\n";
 exit;
}

my $wordfile = $ARGV[0];
my $textfile=$ARGV[3];
my $OutPutFile=$ARGV[4];

open (IF1,"$wordfile")|| die "cannot open the file";
open (PF, "$textfile")|| die "cannot open the file";
open (OF,">$OutPutFile")|| die "cannot open the file";

my $List1Ref=ReadDataInHash (*IF1);



while (my $line=<PF>) {
    chomp($line);
    my @arrAbs=split (/\|/,$line);
    my $ID=$arrAbs[0];
    my $Title=$arrAbs[1];
    my $Abs=$arrAbs[2];
    @arrAbs=split (/\./,$Abs);
    print OF"$ID|";

    for (my $SentenceNumber=0;$SentenceNumber<=$#arrAbs ;$SentenceNumb
+er++) {
        my $i=$SentenceNumber+1;
        print OF "<".$i.">";
        my $Sentence=$arrAbs[$SentenceNumber];
        my @arrAbsSen=split (' ',$Sentence);

        foreach my $word(@arrAbsSen) {

#to match terms in the list, stored in %{$List1Ref}.
            if (exists(${%{$List1Ref}}{uc($word)})) { 
                print OF "$word ";
            }
            
            else {
                foreach my $p (sort keys (%{$List1Ref})) {
                    if (exists(${%{${%{$List1Ref}}{$p}}}{uc($word)})) 
+{ 
                        print OF "mainterm:$p:matchedterm:$word ";
                        last; 
                    }
                }
            }
        }
    @arrAbsSen=();
    }
    print OF "\n";
    @arrAbs=();
}


sub ReadDataInHash()
{
    my $x = shift;
    my %list1=();
    while (my $line =<$x>) {
        chomp $line;
        my @arr=split /\s/,$line;
        for (my $i=0;$i<=$#arr ;$i++) {
            if ($i==0) {
                $list1{$arr[$i]}={};
            }
            else{
                ${%{$list1{$arr[0]}}}{$arr[$i]} = 1;
            }
        }
    }
    return {%list1};
}
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