usage extract-seq.pl file1 file2
cat file1
AV12349
J234054
   .
   .
cat file2
>AV12349
AAACCGTACCTAGAACAGTA
ACAGTACA
>J434594
ACCGTTAGTACGATACA
    .
    .

##</code><code>##

#!/usr/bin/perl

$output = "extracted.seqs";

open (OUT,">$output") or die;

# create names lookup table from first file
while (<>) {
    chomp;
    $names{$_} = 1;
    last if eof;
}
$/ = "\n>";  # set input record separator

# scan second file
while (<>) {
     s/^>//;  #remove leading ">"
     s/>$//;  #remove trailing ">"

     if (/^([\w\d]+)/ && $names{$1}) { print OUT ">$_";}

}