Blast中文手册(1)补充

Limiting a Search by taxonomy(按分类法限制搜索)

Created: June 23, 2008; Updated: January 7, 2021.
In order to limit a BLAST search by taxonomy, one needs to provide the NCBI taxonomy ID(s) (taxid) for given organism(s). A taxid is simply a number that specifies a node in the taxonomic tree. For example, 9606 is the taxid for human, 9989 is the taxid for rodentia, and 2 is the taxid for all bacteria. Taxids are preferable to organism names as the latter can be ambiguous. For instance, bacteria is both a genus of insects as well as a superkingdom. BLAST only accepts taxids that are at or below the species level.

为了按分类法限制BLAST搜索，需要为给定生物体提供NCBI分类法ID（taxid）。taxid只是一个指定分类树中节点的数字。例如，9606是人类的taxid，9989是啮齿动物的taxid，2是所有细菌的taxid。Taxids比有机体名称更可取，因为后者可能模棱两可。例如，细菌既是昆虫的一个属，也是一个超级王国superkingdom。BLAST只接受处于或低于物种水平的taxids。

The BLAST+ command line tool suite provides the get_species_taxids.sh script to translate higher level taxids (e.g.: Enterobacterales) into a list of taxids that are at the appropriate level. This script can also be used to look up (and disambiguate) taxids based upon a taxonomic name. If unsure whether your taxid is at the species level or lower, it is safe to run get_species_taxids.sh and feed the output to BLAST.

BLAST+命令行工具套件提供 get_species_taxids.sh 脚本将更高级别的分类（如肠杆菌）转换为适当级别的分类列表。该脚本还可以用于根据分类名称查找（和消除歧义）分类。如果不确定您的taxid是否处于物种级别或更低级别，则运行get_species_taxids.sh并将输出馈送至BLAST。

Additionally, one may use the -negative_taxids and -negative_taxidlist options to exclude sequences by taxid.

此外，可以使用**-negative_taxids**和 -negative_taxidlist选项按taxid排除序列。

Note: this script depends on EDirect and it only works on Linux and Mac. For EDirect installation instructions, please see https://www.ncbi.nlm.nih.gov/books/NBK179288/ .

注意：此脚本依赖于EDirect，仅适用于Linux和Mac。有关EDirect安装说明，请参阅https://www.ncbi.nlm.nih.gov/books/NBK179288/ .

Limiting a BLAST search with a high-level taxonomic node(使用高级分类节点限制BLAST搜索)

Limiting a BLAST search with a species-level taxonomic node(使用物种级分类节点限制BLAST搜索)

blastn –db nt –query QUERY –taxids 9606 –outfmt 7 –out OUTPUT.tab

Limiting a Search with a List of Identifiers(使用标识符列表限制搜索)

Created: June 23, 2008; Updated: January 7, 2021.
BLAST can also limit a database search by a list of identifiers (e.g.: accessions), which should be specified one per line in a file. These identifiers, referencing the sequences to include or exclude in the BLAST search, should not contain any whitespace and should be retrievable from the BLAST database.

BLAST还可以通过标识符列表（例如：访问）来限制数据库搜索，应该在文件中每行指定一个标识符。这些标识符引用要在BLAST搜索中包括或排除的序列，不应包含任何空格，并且应可从BLAST数据库中检索。

Starting with BLASTDB version 5, an accession list must be pre-processed before it can be used in a search. This process checks that the accessions appear to be real and produces a file optimized for use with BLAST. It is also possible to confirm that all the accessions are actually in the target database. The examples below demonstrate this functionality:

从BLASTDB版本5开始，必须先对登录列表进行预处理，然后才能将其用于搜索。该过程检查访问是否真实，并生成一个为BLAST使用而优化的文件。还可以确认所有访问实际上都在目标数据库中。下面的示例演示了此功能：

Additionally, one may use the -negative_seqidlist option to exclude sequences by accession from the BLAST search.

此外，可以使用-negative_sekidlist选项从BLAST搜索中排除通过加入的序列。

When the search is limited by a list of IDs the statistics of the BLAST database are re-calculated to reflect the actual number of sequences and residues/bases included in the search.

当搜索受到ID列表的限制时，将重新计算BLAST数据库的统计信息，以反映搜索中包含的序列和残基/碱基的实际数量。