Blast比对软件怎么用

这篇文章主要介绍"Blast比对软件怎么用"，在日常操作中，相信很多人在Blast比对软件怎么用问题上存在疑惑，小编查阅了各式资料，整理出简单好用的操作方法，希望对大家解答"Blast比对软件怎么用"的疑惑有所帮助！接下来，请跟着小编一起来学习吧！

Blast比对软件大概是是短序列局部比对软件中最常用的一个了，但是其参数众多，一些参数一直没好好仔细研究过，如下： #### 增加blast比对结果信息

blast的-outfmt参数，使blastp -help即可查看每个输出格式的信息，如下所示：

*** Formatting options -outfmt    alignment view options:     0 = Pairwise,     1 = Query-anchored showing identities,     2 = Query-anchored no identities,     3 = Flat query-anchored showing identities,     4 = Flat query-anchored no identities,     5 = BLAST XML,     6 = Tabular,     7 = Tabular with comment lines,     8 = Seqalign (Text ASN.1),     9 = Seqalign (Binary ASN.1),    10 = Comma-separated values,    11 = BLAST archive (ASN.1),    12 = Seqalign (JSON),    13 = Multiple-file BLAST JSON,    14 = Multiple-file BLAST XML2,    15 = Single-file BLAST JSON,    16 = Single-file BLAST XML2,    18 = Organism Report   Options 6, 7 and 10 can be additionally configured to produce   a custom format specified by space delimited format specifiers.   The supported format specifiers are:        qseqid means Query Seq-id           qgi means Query GI          qacc means Query accesion       qaccver means Query accesion.version          qlen means Query sequence length        sseqid means Subject Seq-id     sallseqid means All subject Seq-id(s), separated by a ';'           sgi means Subject GI        sallgi means All subject GIs          sacc means Subject accession       saccver means Subject accession.version       sallacc means All subject accessions          slen means Subject sequence length        qstart means Start of alignment in query          qend means End of alignment in query        sstart means Start of alignment in subject          send means End of alignment in subject          qseq means Aligned part of query sequence          sseq means Aligned part of subject sequence        evalue means Expect value      bitscore means Bit score         score means Raw score        length means Alignment length        pident means Percentage of identical matches        nident means Number of identical matches      mismatch means Number of mismatches      positive means Number of positive-scoring matches       gapopen means Number of gap openings          gaps means Total number of gaps          ppos means Percentage of positive-scoring matches        frames means Query and subject frames separated by a '/'        qframe means Query frame        sframe means Subject frame          btop means Blast traceback operations (BTOP)        staxid means Subject Taxonomy ID      ssciname means Subject Scientific Name      scomname means Subject Common Name    sblastname means Subject Blast Name     sskingdom means Subject Super Kingdom       staxids means unique Subject Taxonomy ID(s), separated by a ';'             (in numerical order)     sscinames means unique Subject Scientific Name(s), separated by a ';'     scomnames means unique Subject Common Name(s), separated by a ';'    sblastnames means unique Subject Blast Name(s), separated by a ';'             (in alphabetical order)    sskingdoms means unique Subject Super Kingdom(s), separated by a ';'             (in alphabetical order)         stitle means Subject Title    salltitles means All Subject Title(s), separated by a '<>'       sstrand means Subject Strand         qcovs means Query Coverage Per Subject       qcovhsp means Query Coverage Per HSP        qcovus means Query Coverage Per Unique Subject (blastn only)

其实我们一般常用的就是-outfmt 5或者-outfmt 6，前者输出XML格式，后者输出TAB分割格式；前者信息比较全，用处也相对比较广，而后者则是平时最为常用的格式（也是一些软件喜欢调用的格式）

TAB格式每列信息如下（可以对照上面的说明理解一下）：

qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore

但我们有时想要的并不止上述12列信息，比如我还想知道比对结果的覆盖度信息（qcovs：Query Coverage Per Subject）

其实只要在blast比对命令中先事先加上需要增加的列ID即可，如在outfmt 6基础上加上覆盖度信息：

    -outfmt "6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qcovs"

注：需要几列就一直往上加即可，空格分割

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