Linux command
makeblastdb 命令
文本
复制后可按需替换文件名、目录或参数。
常用示例
Create nucleotide database
makeblastdb -in [sequences.fasta] -dbtype nucl -out [mydb]
Create protein database
makeblastdb -in [proteins.fasta] -dbtype prot -out [mydb]
Add title to database
makeblastdb -in [sequences.fasta] -dbtype nucl -title "[My Database]" -out [mydb]
Parse sequence IDs
makeblastdb -in [sequences.fasta] -dbtype nucl -parse_seqids -out [mydb]
Create with taxonomy
makeblastdb -in [sequences.fasta] -dbtype nucl -taxid_map [taxid.map] -out [mydb]
说明
makeblastdb creates BLAST databases from FASTA sequences. These databases are required for running local BLAST searches with blastn, blastp, blastx, and related programs. The resulting database consists of multiple files with extensions like .nhr, .nin, .nsq for nucleotide or .phr, .pin, .psq for protein.
参数
- -in _file_
- Input FASTA file.
- -dbtype _type_
- nucl (nucleotide) or prot (protein).
- -out _name_
- Database name prefix.
- -title _title_
- Database title.
- -parse_seqids
- Parse sequence identifiers.
- -taxid_map _file_
- Taxonomy mapping file.
- -hash_index
- Create hash index.
FAQ
What is the makeblastdb command used for?
makeblastdb creates BLAST databases from FASTA sequences. These databases are required for running local BLAST searches with blastn, blastp, blastx, and related programs. The resulting database consists of multiple files with extensions like .nhr, .nin, .nsq for nucleotide or .phr, .pin, .psq for protein.
How do I run a basic makeblastdb example?
Run `makeblastdb -in [sequences.fasta] -dbtype nucl -out [mydb]` in a terminal, then adjust file names, paths, flags, or remote targets for your system.
What does -in _file_ do in makeblastdb?
Input FASTA file.