Makeblastdb parameters in blast+

All relevant blast operations used in future work are done with blast+.

With the previous blast, we are still starting from the format database to the match

Generally we have a Fasta file used to format the database, the previous command is FORMATDB, and now it is MAKEBLASTDB

The general format used is as follows:

Makeblastdb-in input_file-dbtype molecule_type-title database_title-parse_seqids-out database_name-logfile File_ Name

-in followed by input file, you want to format the Fasta sequence

-dbtype followed by sequence type, Nucl as nucleic acid, prot as protein

-title give the database a name, good-looking ~ ~ (can not be used in the subsequent search-db parameters)

-parse_seqids recommendation Plus, now for what reason is not clear

-out after the database name, you start a meaningful name, and later blast+ search to use the parameters of-db

-logfile log file, if there is no default output to the screen

And the previous formatdb difference is quite big, hehe

Using the Makeblastdb connection parameter-help will print out the information:

Makeblastdb-help
USAGE
Makeblastdb [-h] [-help] [-in input_file] [-dbtype Molecule_type]
[-title Database_title] [-parse_seqids] [-hash_index]
[-mask_data Mask_data_files] [-out database_name]
[-MAX_FILE_SZ Number_of_bytes] [-taxid Taxid] [-taxid_map Taxidmapfile]
[-logfile file_name] [-version]

DESCRIPTION
Application to create BLAST databases, version 2.2.23+

OPTIONAL ARGUMENTS
-H
Print USAGE and DESCRIPTION; Ignore other arguments
-help
Print USAGE, DESCRIPTION and ARGUMENTS DESCRIPTION; Ignore other arguments
-version
Print version number; Ignore other arguments

Input Options
-in <File_In>
Input file/database name; The data type is automatically detected, it may
Be any of the following:
FASTA file (s) and/or
BLAST Database (s)
Default = '-'
-dbtype <string, ' nucl ', ' prot ' >
Molecule type of input
Default = ' Prot '

Configuration Options
-title <String>
Title for BLAST Database
Default = input file name provided to-in argument
-parse_seqids
Parse seq-ids in FASTA input
-hash_index
Create index of sequence hash values.

Sequence Masking Options
-mask_data <String>
comma-separated List of input files containing masking data as produced by
NCBI masking applications (e.g. Dustmasker, Segmasker, Windowmasker)

Output Options
-out <String>
Name of BLAST database to be created
Default = input file name provided to-in argumentrequired if multiple
File (s)/database (s) is provided as input
-MAX_FILE_SZ <String>
Maximum file size for BLAST database files
Default = ' 1GB '

Taxonomy options
-taxid <integer, >=0>
Taxonomy ID to assign to all sequences
* Incompatible With:taxid_map
-taxid_map <File_In>
Text file mapping sequence IDs to taxonomy IDs.
Format:<sequenceid> <TaxonomyId><newline>
* Incompatible WITH:TAXID
-logfile <File_Out>
File to which the program log should is redirected

Makeblastdb parameters in blast+