if you have less time, then use three ways mentioned in bookmark link to extract/download all fasta sequences in single click given that you already have a list of GIs or accession IDs .
Alternatively, use one liner perl script:
perl -ne 'if(/^>(\S+)/){$c=$i{$1}}$c?print:chomp;$i{$_}=1 if @ARGV' GIs.txt >sequence.fasta
where GIs.txt contains a list of GIs or accession IDs.
(from :http://edwards.sdsu.edu/labsite/index.php/robert?start=5)
