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Usage-env09-ncbi.md

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This page introduces the usages in the environment of 'ncbi'.

Updated on 2023-07-28

Usage description

Usage text

  # annotation
  (environment) ~/location$ command line

Move to your workplace and activate the environment first

  # don't forget to change to your directory first
  (base) jiang@azur:~$ cd user_name
  
  # check the current environment at the beginning of the command line, like the 'base' here
  (base) jiang@azur:~/user_name$
  # if not the target environment, activate it by 'conda activate'
  (base) jiang@azur:~/user_name$ conda activate ncbi
  # check again at the beginning, now it is 'ncbi', good to go
  (ncbi) jiang@azur:~/user_name$

Here mainly introduce two tools for local blast:

  • NCBI blast+
  • DIAMOND (optimized for large input files of >1 million proteins)

NCBI blast+

#for protein

(ncbi) jiang@azur:~/user_name$ makeblastdb -dbtype prot -hash_index -parse_seqids -in DATABASE.faa
(ncbi) jiang@azur:~/user_name$ blastp -evalue 0.01 -outfmt 6 -db DATABASE.faa -query QUERY.faa  -out OUTPUT.txt

#for nucleic acid

(ncbi) jiang@azur:~/user_name$ makeblastdb -dbtype nucl -hash_index -parse_seqids -in DATABASE.fna
(ncbi) jiang@azur:~/user_name$ blastn -evalue 0.01 -outfmt 6 -db DATABASE.fna -query QUERY.fna  -out OUTPUT.txt

*Format of outfmt6:

query acc.ver, subject acc.ver, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score

DIAMOND

#create a diamond-formatted database file

(ncbi) jiang@azur:~/user_name$ diamond makedb --in reference.fasta -d reference

#run a blast search

# blastp mode
(ncbi) jiang@azur:~/user_name$ diamond blastp -d reference -q queries.fasta -o matches.tsv
# blastx mode
(ncbi) jiang@azur:~/user_name$ diamond blastx -d reference -q reads.fasta -o matches.tsv