NCBI本地Blast 安装方法.doc

IN HOUSE LOCAL BLAST SEARCHTo get started you need the blastall.exe and formatdb.exe (From NCBI). The rest of the perl and batch programs you might need to change the path of the directories they are pointing to or the blast option they use, could be downloaded from: /SGMD/software/blast/Blast.htmFor the programs to work without modifying the paths, the whole folder “Blast.zip” should be unzipped to a folder Blast moved under the “C:” directory. For questions or comments please contact: Imed Ben CI. Step one: Blasting1) Download the database that you want to blast against, for example the NT database from NCBI. If you want to use a local database, store all the sequences in a text file.The file provided by NCBI is a zipped (nt.gz) file so you have to unzip it.2) At the DOS prompt (which you can get to from windows by choosing: Start, Run, then typing: command), run formatdb.exe to create a local database from that text file or the downloaded database. Usage:formatdb t databasename i inputfile p FExamples: 1)formatdb t nt i nt p F2) formatdb t snc i inputfile p Fdatabasename is the name you want to give to your databaseinputfile is the name of the text file that contains your sequences or the name of the database that you downloaded from GenBank (technically also a text file of sequences).More about formatdb.exe information and command options can be found here:/IEB/ToolBox/C_DOC/lxr/source/doc/formatdb.txt3) Open the file BlastList.pl (using Notepad or your favorite text editor)Make the small changes as instructed in the file then save it.These are the only two changes that should be made to run the program.4) Run BlastList.pl as follows:c: cd Blastc:Blastperl BlastList.plThe file BlastList.pl automatically creates a batch file “DosBlast.bat” depending on the list of the sequence to be blasted.5) Run DosBlast.batc:Blast DosBlast.batDosBlast.bat is the actual file that does the blast search.II. Step two: Extracting data from blast results6) Move all the resulting .txt files to BlastOut7) Go to the directory BlastOutc:Blast cd BlastOut8) Run Hits.pl c:BlastBlastOutperl Hits.plThat will move the files that returned no hits to a different directory9) Run DataExt.plc:BlastBlastOutperl DataExt.plThe output will be written to the file Blasted.txt.With Excel open (using tab delimited) the file Blasted.txt. It contains a summary of the blast results that you can save, edit, etc.LIST OF PROGRAMS: The required programs are available in this directory but here is the code for four of them in case you wish to make some modifications:1) BlastList.bat2) DosBlast.bat3) Hits.pl4) DataExt.pl=BlastList.bat=#!/usr/local/bin/perl# file: BlastList.pl# # Imed Ben Chouikha # 04/24/03# # This files creates a batch file DosBlast.bat based on # the list of .seq sequence files.# The file DosBlast.Bat runs separetly. (For more information see ReadMe.doc)# send comments to: # CHANGES TO MAKE# 1) Change SCN_seq.fas (in the first line of the program) with the name of the local # database you are Blasting against:# 2) eliminate (only if needed) anything other than the sequence files in the #unless statement (below, in the middle of the code).$DBNAME = SCN_seq.fas; # Replace SCN_seq.fas with local Database name$dirtoget=C:/Blast;opendir(IMD, $dirtoget) | die(Cannot open directory);# delete the old DosBlast.bat file that contains the list of sequences# to be blasted$dosfile = DosBlast.bat;unlink($dosfile);# Get the list of the new sequence files to blastthefiles= readdir(IMD);closedir(IMD);# Create a new file DosBlast.bat open(OUT,DosBlast.bat) | die cannot open file for writing: $!;foreach $f (thefiles) # Add to the list below everything other that the sequence files # Here is the Unless statement: unless ( ($f eq .) | ($f eq .) | ($f eq DosBlast.bat) | ($f eq BlastList.pl) | ($f eq $DBNAME)|($f eq BlastOut) | ($f eq blastall.exe) | ($f eq formatdb.exe)| ($f eq formatdb.log)| ($f eq ReadMe.doc) myarray = split(/./,$f); # Old file name $extension =.txt; # This is the new file extension newname=myarray0.$extension; print(OUT blastall -p blastn -d $DBNAME -i $f -o newname -v 0 -b 1n); # end of unless # end of foreach=DosBlast.bat=# Changed this file to be automatically generated. So you do not have to worry about it# it contains lines of the form # blastall -p blastn -d $DBNAME -i $f -o newname -v 0 -b 1# where $DBNAME is the Database name, $f and newname are the input and output names # read from the directory by BlastList.pl=Hits.pl=#!/usr/local/bin/perl# file Hits.pl# Imed Ben Chouikha# 04/24/03 # This files moves all the files that returned No Hits to the directory called NoHits# and deletes them from the current directory # Send comments to: $dirtoget=C:/Blast/BlastOut;opendir(IMD, $dirtoget) | die(Cannot open directory);thefiles= readdir(IMD);#closedir(IMD);# loop over the filesforeach $f (thefiles) unless ( ($f eq .) | ($f eq .) | ($f eq Blasted.txt) | ($f eq DataExt.pl)| ($f eq NoHits) | ($f eq Hits.pl) open(IN, $f) | die cannot open file for reading: $!;#open(OUT,nohitlist.txt) | die cannot open file for writing: $!;$nohit = No Hits Found;$count = 0; while($lines = ) chop($lines);if ($lines = /$nohit/)$count += 1;else$count = $count;$lines += 1; # end of while loop if ($count = 1)close(IN);$odir=NoHits;opendir(IMD1, $odir) | die(Cannot open directory);rename($f, $odir/$f);closedir(IMD1); #unlink($f); else $count = $count; # end of unless # end of foreachclosedir(IMD);=DataExt.pl=#!/usr/local/bin/perl# file: DataExt.pl# # Imed Ben Chouikha# 04/24/03# # This file extracts the E-values, best hits, and other values from the Blast result.# send comments to: $dirtoget=C:/Blast/BlastOut;opendir(IMD, $dirtoget) | die(Cannot open directory);thefiles= readdir(IMD);closedir(IMD);# loop over the filesopen(OUT,Blasted.txt) | die cannot open file for writing: $!;foreach $f (thefiles) unless ( ($f eq .) | ($f eq .) | ($