I'd build a lookup table then walk over the sentence one word at a time looking for matches:

use strict;
use warnings;

my $sentence = 'The Doc4 protein , stress-induced flibbled the woozle 
+in the presence of gonadotrophin alpha 2 subunit';

my %proteinLU;

while (<DATA>) {
    chomp;

    my $protein = $_;
    my @parts = split;
    my $parent = \%proteinLU;

    while (@parts) {
        my $part = shift @parts;

        $parent = $parent->{$part} ||= {};
        next if @parts;
        $parent->{_name_} = $protein;
    }
}

my @words = split ' ', $sentence;

while (@words) {
    my $word = shift @words;

    next if ! exists $proteinLU{$word};

    my $parent = $proteinLU{$word};
    my $wIndex = 0;

    while ($wIndex < @words && exists $parent->{$words[$wIndex]}) {
        $parent = $parent->{$words[$wIndex++]}
    }

    print "$parent->{_name_}\n" if exists $parent->{_name_};
}


__DATA__
7-phospho-2-dehydro-3-deoxy-D-arabino-heptonate D-erythrose-4-phosphat
+e lyase (pyruvate-phosphorylating)
gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (Gamma-Glu-gamma
+-aminobutyraldehyde dehydrogenase)
3-phosphoshikimate 1-carboxyvinyltransferase (5-enolpyruvylshikimate-3
+-phosphate synthase)(EPSP synthase
Hypothetical protein CBG17340
gonadotrophin alpha 2 subunit
Doc4 protein , stress-induced
optomotor-blind
Dfrizzled-3
Tramtrack69
gutfeeling
betaFTZ-F1
Sex-lethal
Strabismus
PAR3alpha
Armadillo
AP-2alpha
GLUT1CBP
eIF3-p44
Flamingo
PP2Czeta
PLCgamma
TFIIIC90
Wingless
Frizzled
Profilin
TXBP151

[download]

Prints:

Doc4 protein , stress-induced
gonadotrophin alpha 2 subunit

[download]

I invented a sentence because the sample sentence didn't seem to include any of the sample proteins so didn't provide a very interesting test case!

Very likely you will have to normalize the protein names in some fashion and normalize the sentence likewise so that variations in punctuation and white space usage don't prevent valid matches. But you'd have had to do that in any case so I guess you have that sorted out.

True laziness is hard work

In reply to Re^2: Tag protein names in sentences by GrandFather
in thread Tag protein names in sentences by sinlam

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