我们需要对自己的基因做注释，需要blast同源比对NCBI当中的NR NT库；通常做无参转录组，会组织出10几万的unigene ，如果比对全库的话，就太浪费时间了，我们可以根据NCBI的分类数据库将数据库分开，可下载如下文件，然后利用下面的perl脚本就可以把NR或者NT库分开成小库：

wget -c ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz
wget -c ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nt.gz
wget -c ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/gi_taxid_nucl.dmp.gz
wget -c ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/gi_taxid_prot.dmp.gz
wget -c ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz

perl脚本如下，由于脚本会把分类文件全部读入内存，所有脚本内存消耗较大，建议确保100G以上的内存空间：

#The gi_taxid_nucl.dmp is about 160 MB and contains  two columns: the nucleotide's gi and taxid.
#The gi_taxid_prot.dmp is about 17 MB and contains two columns:  the protein's gi  and taxid.

#Divisions file (division.dmp):
#	division id				-- taxonomy database division id
#	division cde				-- GenBank division code (three characters)
#	division name				-- e.g. BCT, PLN, VRT, MAM, PRI...
#	comments




#0       |       BCT     |       Bacteria        |               |
#1       |       INV     |       Invertebrates   |               |
#2       |       MAM     |       Mammals |               |
#3       |       PHG     |       Phages  |               |
#4       |       PLN     |       Plants and Fungi        |               |
#5       |       PRI     |       Primates        |               |
#6       |       ROD     |       Rodents |               |
#7       |       SYN     |       Synthetic and Chimeric  |               |
#8       |       UNA     |       Unassigned      |       No species nodes should inherit this division assignment        |
#9       |       VRL     |       Viruses |               |
#10      |       VRT     |       Vertebrates     |               |
#11      |       ENV     |       Environmental samples   |       Anonymous sequences cloned directly from the environment        |

#nodes.dmp file consists of taxonomy nodes. The description for each node includes the following
#fields:
#        tax_id                                  -- node id in GenBank taxonomy database
#        parent tax_id                           -- parent node id in GenBank taxonomy database
#        rank                                    -- rank of this node (superkingdom, kingdom, ...)
#        embl code                               -- locus-name prefix; not unique
#        division id                             -- see division.dmp file
#        inherited div flag  (1 or 0)            -- 1 if node inherits division from parent
#        genetic code id                         -- see gencode.dmp file
#        inherited GC  flag  (1 or 0)            -- 1 if node inherits genetic code from parent
#        mitochondrial genetic code id           -- see gencode.dmp file
#        inherited MGC flag  (1 or 0)            -- 1 if node inherits mitochondrial gencode from parent
#        GenBank hidden flag (1 or 0)            -- 1 if name is suppressed in GenBank entry lineage
#        hidden subtree root flag (1 or 0)       -- 1 if this subtree has no sequence data yet
#        comments                                -- free-text comments and citations




die "perl $0 <division.dmp> <nodes.dmp> <gi_taxid_n/p.dmp> <nr.fa/nt.fa> <od>" unless(@ARGV==5);

use Math::BigFloat;
use Bio::SeqIO;
use Bio::Seq;
use Data::Dumper;
use PerlIO::gzip;

use FileHandle;


use Cwd qw(abs_path getcwd);
if ($ARGV[3]=~/gz$/){
	open $Fa, "<:gzip", "$ARGV[3]" or die "$!";
}else{
	open $Fa, "$ARGV[3]" or die "$!";
}

my$od=$ARGV[4];

$od||=getcwd;
$od=abs_path($od);
unless(-d $od){	mkdir $od;}


my $in  = Bio::SeqIO->new(-fh => $Fa ,
                               -format => 'Fasta');


my %division2name=();
open IN,"$ARGV[0]" or die "$!";


while(<IN>){
	chomp;
	my($taxid,$name)=split(/\s+\|\s+/);
	$division2name{$taxid}=$name;
}
close(IN);


my%fout=();

for my$i (keys %division2name){
	
	
	
	my$FO=FileHandle->new("> $od/$division2name{$i}.fa");
	
	my $out = Bio::SeqIO->new(-fh => $FO ,  -format => 'Fasta');
	$fout{$i}=$out;

}

print "$ARGV[0] readed\n";

#print Dumper(\%fout);
#print Dumper(\%division2name);

open IN,"$ARGV[1]" or die "$!";

my%taxid2division=();


while(<IN>){
	chomp;
	my@tmp=split(/\s+\|\s+/);
	$taxid2division{$tmp[0]}=$tmp[4];
	#last if $.>100;
}
close(IN);

print "$ARGV[1] readed\n";


my %gi2taxid=();


open IN,"$ARGV[2]" or die "$!";

while(<IN>){
	chomp;
	my@tmp=split(/\s+/);
	$gi2taxid{$tmp[0]}=$tmp[1];
	#last if $.>100;
}
close(IN);


print "$ARGV[2] readed\n";


#print Dumper(\%gi2taxid);

while( my $seq = $in->next_seq()){
	
	my $id=$seq->id;
	my ($gi)=($id=~/gi\|(\d+)\|ref\|/);
	if(exists($gi2taxid{$gi}) and exists($taxid2division{$gi2taxid{$gi}})){
		$fout{$taxid2division{$gi2taxid{$gi}}}->write_seq($seq);
	}else{
		print "unknown gi:$gi\n";
	}
}



for my $i (keys %fout){
	
	$fout{$i}->close();
	
	
}

2021 NCBI又更新:https://www.omicsclass.com/article/1614

更多生物信息课程：https://study.omicsclass.com/index