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Blast+

latest release

Installation

For Ubuntu or Debian (Deepin, like me)

  1. sudo apt-get install ncbi-blast+

For other distributions:

  1. wget -c https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.12.0+-x64-linux.tar.gz
  2. tar -zxvf ncbi-blast-2.12.0+-x64-linux.tar.gz
  3. cd ncbi-blast-2.12.0+/bin

Quick Start

make blast base

  1. makeblastdb -in db.fasta -dbtype prot/nucl -parse_seqids -out dbname

model of uniprot annotation

  1. blastx -query T0.05.fa -out blast.out -db /media/ken/Base/blastdb/uniprot_sprot.fasta -outfmt "6 qacc sacc evalue stitle sblastname" -evalue 1e-5 -max_target_seqs 1 -num_threads 8 -max_hsps 1

Output format

  1. Options 6, 7 and 10 can be additionally configured to produce
  2. a custom format specified by space delimited format specifiers.
  3. The supported format specifiers are:
  4.      qseqid means Query Seq-id
  5.         qgi means Query GI
  6.        qacc means Query accesion
  7.     qaccver means Query accesion.version
  8.        qlen means Query sequence length
  9.      sseqid means Subject Seq-id
  10.   sallseqid means All subject Seq-id(s), separated by a ';'
  11.         sgi means Subject GI
  12.      sallgi means All subject GIs
  13.        sacc means Subject accession
  14.     saccver means Subject accession.version
  15.     sallacc means All subject accessions
  16.        slen means Subject sequence length
  17.      qstart means Start of alignment in query
  18.        qend means End of alignment in query
  19.      sstart means Start of alignment in subject
  20.        send means End of alignment in subject
  21.        qseq means Aligned part of query sequence
  22.        sseq means Aligned part of subjecnit sequence
  23.      evalue means Expect value
  24.    bitscore means Bit score
  25.       score means Raw score
  26.      length means Alignment length
  27.      pident means Percentage of identical matches
  28.      nident means Number of identical matches
  29.    mismatch means Number of mismatches
  30.    positive means Number of positive-scoring matches
  31.     gapopen means Number of gap openings
  32.        gaps means Total number of gaps
  33.        ppos means Percentage of positive-scoring matches
  34.      frames means Query and subject frames separated by a '/'
  35.      qframe means Query frame
  36.      sframe means Subject frame
  37.        btop means Blast traceback operations (BTOP)
  38.      staxid means Subject Taxonomy ID
  39.    ssciname means Subject Scientific Name
  40.    scomname means Subject Common Name
  41.  sblastname means Subject Blast Name
  42.   sskingdom means Subject Super Kingdom
  43.     staxids means unique Subject Taxonomy ID(s), separated by a ';'
  44.       (in numerical order)
  45.   sscinames means unique Subject Scientific Name(s), separated by a ';'
  46.   scomnames means unique Subject Common Name(s), separated by a ';'
  47.  sblastnames means unique Subject Blast Name(s), separated by a ';'
  48.       (in alphabetical order)
  49.  sskingdoms means unique Subject Super Kingdom(s), separated by a ';'
  50.       (in alphabetical order)
  51.      stitle means Subject Title
  52.  salltitles means All Subject Title(s), separated by a '<>'
  53.     sstrand means Subject Strand
  54.       qcovs means Query Coverage Per Subject
  55.     qcovhsp means Query Coverage Per HSP
  56.      qcovus means Query Coverage Per Unique Subject (blastn only)

Enjoy~

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