Hi, I have tried the following code for substring search, but it still only works for full strings: 
open (GEN, "<general.txt") || die ("cannot open general.txt");
open (SEA, "<search.txt") || die ("cannot open search.txt");

undef $/;

$gen = <GEN>;
$sea = <SEA>;
@gen = split /\n/, $gen;
@sea = split /\n/, $sea;

for $a (@gen)
{
# no SUBSTRINGS:  @result = grep/^\Q$a\E$/, @sea;
    @result = grep/\Q$a\E/, @sea;
    push (@final , @result);
}

print "Search string that matches against general data:\t@final";

[download]
////////////////////////////////////////////////////////// here is the content of 'general.txt': AT1G01450 AT1G12680 AT1G20650 AT1G30640 AT1G33770 AT1G49580 AT1G50140 ////////////////////////////////////////////////////////// here is the content of 'search.txt': At1g28530 At1g28530 At1g55090 At2g14580 1450 ////////////////////////////////////////////////////////// the program should recognize '1450' as substring of the first line of 'general.txt' and give out the whole first line of 'general.txt', right? Jurgen

In reply to Re^4: compare two text files by juergenkemeter
in thread compare two text files by juergenkemeter

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