BLAST Command Line Applications User Manual

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Page 164.6.12.1 dir: Name of the directory where to look for BLAST databases.4.6.12.2 recursive: Flag to specify whether to recursively search for BLAST databases in thedirectory specified above.4.6.12.3 full: Check every database sequence.BLAST Help BLAST Help BLAST Help BLAST Help4.6.13 blast_formatter4.7 Configuring BLAST4.6.12.4 stride: Check every Nth database sequence.4.6.12.5 samples: Check a randomly selected set of N sequences.4.6.12.6 ends: Check the beginning and ending N sequences in the database.4.6.12.7 isam: Set to true to perform ISAM file checking on each of the selected sequences.This application formats both local and remote BLAST results. An RID is required to formatremote BLAST results. The RID may be obtained either from a search submitted to the NCBIBLAST web page or by using the –remote switch with one of the applications mentioned above.The blast_formatter accepts the BLAST archive format for stand-alone formatting. TheBLAST archive format can be produced by using “-outfmt 11” argument with the stand-aloneapplications. The following are its supported options:4.6.13.1 rid: BLAST RID of the report to be formatted.4.6.13.2 archive: File produced by BLAST application using –outfmt 11The BLAST+ search applications can be configured by means of a configuration filenamed .ncbirc (on Unix-like platforms) or ncbi.ini (on Windows). This is a plain text file whichcontains sections and key-value pairs to specify configuration parameters. Lines starting witha semi-colon are considered comments. This file will be searched in the following order andlocations:1 Current working directory2 User's HOME directory3 Directory specified by the NCBI environment variableThe search for this file will stop at the first location where it is found and the configurationssettings from that file will be applied. If the configuration file is not found, default values willapply. The following are the possible configuration parameters that impact the BLAST+applications:BLAST Command Line Applications User Manual
Page 17Configuration Parameter Specifies Default valueBLASTDB Path to BLAST databases. Current working directoryBLAST Help BLAST Help BLAST Help BLAST HelpDATA_LOADERSBLASTDB_PROT_DATA_LOADERBLASTDB_NUCL_DATA_LOADERData loaders to use for automatic sequence identifier resolution. This is acomma separated list of the following keywords: blastdb, genbank, andnone. The none keyword disables this feature and takes precedence overany other keywords specified.Locally available BLAST database name to search when resolving proteinsequences using BLAST databases. Ignored if DATA_LOADERS doesnot include the blastdb keyword.Locally available BLAST database name to search when resolvingnucleotide sequences using BLAST databases. Ignored ifDATA_LOADERS does not include the blastdb keyword.blastdb,genbankGENE_INFO_PATH Path to gene information files (NCBI only). Current working directoryWINDOW_MASKER_PATH Path to windowmasker files (experimental). Current working directoryThe following is an example with comments describing the available parameters forconfiguration:; Start the section for BLAST configuration[BLAST]4.7.1 Memory usage5. Cookbook; Specifies the path where BLAST databases are installedBLASTDB=/home/guest/blast/db; Specifies the data sources to use for automatic resolution; for sequence identifiersDATA_LOADERS=blastdb; Specifies the BLAST database to use resolve protein sequencesBLASTDB_PROT_DATA_LOADER=custom_protein_database; Specifies the BLAST database to use resolve protein sequencesBLASTDB_NUCL_DATA_LOADER=/home/some_user/my_nucleotide_db; Windowmasker settings (experimental)[WINDOW_MASKER]WINDOW_MASKER_PATH=/home/guest/blast/db/windowmasker; end of fileThe BLAST search programs can exhaust all memory on a machine if the input is too large orif there are too many hits to the BLAST database. If this is the case, please see your operatingsystem documentation to limit the memory used by a program (e.g.: ulimit on Unix-likeplatforms).5.1 Query a BLAST database with a GI, but exclude that GI from the resultsExtract a GI from the ecoli database:$ blastdbcmd -entry all -db ecoli -dbtype nucl -outfmt %g | head -1 | \tee exclude_me1786181Run the restricted database search, which shows there are no self-hits:$ blastn -db ecoli -negative_gilist exclude_me -show_gis -num_alignments 0 \nrntBLAST Command Line Applications User Manual
Page 1 and 2: BLAST Command Line Applications Use
Page 3 and 4: Page 33. Quick startBLAST Help BLAS
Page 5 and 6: Page 54.2.6 db_soft_mask: Filtering
Page 7 and 8: Page 7The legacy_blast.pl script su
Page 9 and 10: Page 9est.500.in -outfmt 7 -out new
Page 11 and 12: Page 114.6 Options by program type4
Page 13: Page 134.6.8.1 in: Input file or BL
Page 18 and 19: Page 18-query exclude_me | grep `ca
Page 20 and 21: Page 20Here the input is hs_chr.mfa
Page 22 and 23: Page 22Using blastdbcmd, we can che
Page 24 and 25: Page 24In a test run under a 64-bit
Page 26 and 27: c. In a private termination action,
Page 28 and 29: Page 28BLAST Help BLAST Help BLAST
Page 30: Page 30type of the BLAST database.

BLAST Command Line Applications User Manual

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