NCBI Blast+的本地安装与使用

NCBI Blast是常用的序列查找工具, 包括蛋白, 核酸. 一般使用网页进行查询即可, 但有时候开发则需要本地的数据库以及程序. NCBI提供Blast+工具包, 内含多种blast工具, 介绍可以参考NCBI提供的两份文档(书):

• BLAST® Command Line Applications User Manual
• BLAST® Help

下载与安装

Blast+的下载

• Blast+程序下载: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
• 根据平台进行选择安装, 例如mac的dmg版本, win的-win64.exe.
• Mac安装后再/usr/local/ncbi/blast
• 安装目录内含有两个子文件夹, bin与doc. bin内有可执行程序, 介绍如下:

Program	Function
blastdbcheck	Checks the integrity of a BLAST database
blastdbcmd	Retrieves sequences or other information from a BLAST database
blastdb_aliastool	Creates database alias (to tie volumes together for example)
Blastn	Searches a nucleotide query against a nucleotide database
blastp	Searches a protein query against a protein database
blastx	Searches a nucleotide query, dynamically translated in all six frames, against a protein database
blast_formatter	Formats a blast result using its assigned request ID (RID) or its saved archive
convert2blastmask	Converts lowercase masking into makeblastdb readable data
deltablast	Searches a protein query against a protein database, using a more sensitive algorithm
dustmasker	Masks the low complexity regions in the input nucleotide sequences
legacy_blast.pl	Converts a legacy blast search command line into blast+ counterpart and execute it
makeblastdb	Formats input FASTA file(s) into a BLAST database
makembindex	Indexes an existing nucleotide database for use with megablast
makeprofiledb	Creates a conserved domain database from a list of input position specific scoring matrix (scoremats) generated by psiblast
psiblast	Finds members of a protein family, identifies proteins distantly related to the query, or builds position specific scoring matrix for the query
rpsblast	Searches a protein against a conserved domain database to identify functional domains present in the query
rpstblastn	Searches a nucleotide query, by dynamically translating it in all six-frames first, against a conserved domain database
segmasker	Masks the low complexity regions in input protein sequences
tblastn	Searches a protein query against a nucleotide database dynamically translated in all six frames
tblastx	Searches a nucleotide query, dynamically translated in all six frames, against a nucleotide database similarly translated
update_blastdb.pl	Downloads preformatted blast databases from NCBI
windowmasker	Masks repeats found in input nucleotide sequences

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executables 除了提供 Blast+, 还提供其他工具:

• magic-blast : 用于映射大的next-generation RNA和DNA序列到全基因组或转录组的. 可参考Magic-Blast
• IgBlast : 分析免疫球蛋白和T细胞受体可变区域序列. 可参考IgBlast 和相关文献.
• rmblast :
• remote-fuser :

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配置

1. 将BLAST按照目录export到PATH, 例如 export PATH=$PATH:$HOME/ncbi-blast-2.8.1+/bin. 这可保证直接执行.
2. 管理数据库:

• 创建一个存放数据库的文件夹: mkdir $HOME/ncbi-blast-2.8.1+/blastdb
• 设置BLASTDB环境变量, export BLASTDB=$HOME/blastdb
• 自行下载和解压相关序列数据库
• 使用updata_blastdb.pl来管理数据库.

数据库的下载

NCBI FTP服务器提供一个BLAST的专门文件夹 : ftp://ftp.ncbi.nlm.nih.gov/blast/, 含有BLAST程序以及数据库. 内含以下子文件夹:

• db : 数据库, 很重要
• executables : 可执行程序, 包括Blast+
• documents : 文档
• demo : 各种提供给开发者的demonstration packages
• matrices : Different supported and experimental scoring matrices
• WGS_TOOLS : 产生WGS计划数据库的工具
• temp : 杂项文件
• windowmasker_files : A collection of windowmasker files for various organisms/genomes, each in its own subdirectory named using their taxonomic ids

配置

可执行文件路径加入到环境变量. 将blast内bin的文件夹路径加入到PATH环境变量即可, 请自行搜索具体方法. 例如Bash: export PATH=$PATH:/usr/local/ncbi/blast/bin

另外一个重要的配置是BLASTDB环境变量, 即blast进行搜索时数据库所在. 根据数据库位置进行设置, 例如 : export BLASTDB=$HOME/blastdb

示例

官方简单示例1

• 使用blastdbcmd提取已安装数据库(refseq_rna.00)中的nm_000122序列到文档test_query.txt
• 运行blastn进行核酸的搜索, 也是搜索本地该数据库.

Standalone BLAST Setup for Unix 内的例子

$ blastdbcmd -db refseq_rna.00 -entry nm_000122 -out test_query.fa
$ blastn -query test_query.fa -db refseq_rna.00 -task blastn -dust no -outfmt "7 qseqid sseqid evalue bitscore" -max_target_seqs 2
# BLASTN 2.2.29+
# Query: gi|263191547|ref|NM_000122.3| Homo sapiens mutL homolog 1 (MLH1), transcript variant 1, mRNA
# Database: refseq_rna.00
# Fields: query id, subject id, evalue, bit score
# 2 hits found
gi|263191547|ref|NM_000122.3|   gi|263191547|ref|NM_000122.3|   0.0      4801
gi|263191547|ref|NM_000122.3|   gi|332816398|ref|XM_001170433.2|        0.0      4758
# BLAST processed 1 queries