USAGE blastdbcmd [-h] [-help] [-db dbname] [-dbtype molecule_type] [-entry sequence_identifier] [-entry_batch input_file] [-pig PIG] [-info] [-range numbers] [-strand strand] [-mask_sequence_with mask_algo_id] [-out output_file] [-outfmt format] [-target_only] [-get_dups] [-line_length number] [-ctrl_a] [-show_blastdb_search_path] [-list directory] [-remove_redundant_dbs] [-recursive] [-list_outfmt format] [-exact_length] [-long_seqids] [-logfile File_Name] [-version] DESCRIPTION BLAST database client, version 2.7.1+ OPTIONAL ARGUMENTS -h Print USAGE and DESCRIPTION; ignore all other parameters -help Print USAGE, DESCRIPTION and ARGUMENTS; ignore all other parameters -version Print version number; ignore other arguments *** BLAST database options -db BLAST database name Default = `nr' * Incompatible with: list, recursive, remove_redundant_dbs, list_outfmt, show_blastdb_search_path -dbtype Molecule type stored in BLAST database Default = `guess' *** Retrieval options -entry Comma-delimited search string(s) of sequence identifiers: e.g.: 555, AC147927, 'gnl|dbname|tag', or 'all' to select all sequences in the database * Incompatible with: entry_batch, pig, info, list, recursive, remove_redundant_dbs, list_outfmt, show_blastdb_search_path -entry_batch Input file for batch processing (Format: one entry per line, seq id followed by optional space-delimited specifier(s) [range|strand|mask_algo_id] * Incompatible with: entry, range, strand, mask_sequence_with, pig, info, list, recursive, remove_redundant_dbs, list_outfmt, show_blastdb_search_path -pig =0> PIG to retrieve * Incompatible with: entry, entry_batch, target_only, info, list, recursive, remove_redundant_dbs, list_outfmt, show_blastdb_search_path -info Print BLAST database information * Incompatible with: entry, entry_batch, outfmt, strand, target_only, ctrl_a, get_dups, pig, range, mask_sequence, list, remove_redundant_dbs, recursive, list_outfmt, list, recursive, remove_redundant_dbs, list_outfmt, show_blastdb_search_path, long_seqids *** Sequence retrieval configuration options -range Range of sequence to extract in 1-based offsets (Format: start-stop, for start to end of sequence use start - ) * Incompatible with: entry_batch, info, list, recursive, remove_redundant_dbs, list_outfmt, show_blastdb_search_path -strand Strand of nucleotide sequence to extract Default = `plus' * Incompatible with: entry_batch, info, list, recursive, remove_redundant_dbs, list_outfmt, show_blastdb_search_path -mask_sequence_with Produce lower-case masked FASTA using the algorithm ID specified * Incompatible with: entry_batch *** Output configuration options -out Output file name Default = `-' -outfmt Output format, where the available format specifiers are: %f means sequence in FASTA format %s means sequence data (without defline) %a means accession %g means gi %o means ordinal id (OID) %i means sequence id %t means sequence title %l means sequence length %h means sequence hash value %T means taxid %X means leaf-node taxids %e means membership integer %L means common taxonomic name %C means common taxonomic names for leaf-node taxids %S means scientific name %N means scientific names for leaf-node taxids %B means BLAST name %K means taxonomic super kingdom %P means PIG %m means sequence masking data. Masking data will be displayed as a series of 'N-M' values separated by ';' or the word 'none' if none are available. If '%f' is specified, all other format specifiers are ignored. For every format except '%f', each line of output will correspond to a sequence. Default = `%f' * Incompatible with: info, list, recursive, remove_redundant_dbs, list_outfmt, show_blastdb_search_path -target_only Definition line should contain target entry only * Incompatible with: pig, info, get_dups, list, recursive, remove_redundant_dbs, list_outfmt, show_blastdb_search_path -get_dups Retrieve duplicate accessions * Incompatible with: info, target_only, list, recursive, remove_redundant_dbs, list_outfmt, show_blastdb_search_path *** Output configuration options for FASTA format -line_length =1> Line length for output Default = `80' * Incompatible with: list, recursive, remove_redundant_dbs, list_outfmt, show_blastdb_search_path -ctrl_a Use Ctrl-A as the non-redundant defline separator * Incompatible with: info, list, recursive, remove_redundant_dbs, list_outfmt, show_blastdb_search_path *** BLAST database configuration and discovery options -show_blastdb_search_path Displays the default BLAST database search paths * Incompatible with: entry, entry_batch, outfmt, strand, target_only, ctrl_a, get_dups, pig, range, db, info, mask_sequence, line_length, list, recursive, list_outfmt, remove_redundant_dbs -list List BLAST databases in the specified directory * Incompatible with: info, entry, entry_batch, outfmt, strand, target_only, ctrl_a, get_dups, pig, range, db, info, mask_sequence, line_length, show_blastdb_search_path -remove_redundant_dbs Remove the databases that are referenced by another alias file in the directory in question * Incompatible with: info, entry, entry_batch, outfmt, strand, target_only, ctrl_a, get_dups, pig, range, db, info, mask_sequence, line_length, show_blastdb_search_path -recursive Recursively traverse the directory structure to list available BLAST databases * Incompatible with: info, entry, entry_batch, outfmt, strand, target_only, ctrl_a, get_dups, pig, range, db, info, mask_sequence, line_length, show_blastdb_search_path -list_outfmt Output format for the list option, where the available format specifiers are: %f means the BLAST database absolute file name path %p means the BLAST database molecule type %t means the BLAST database title %d means the date of last update of the BLAST database %l means the number of bases/residues in the BLAST database %n means the number of sequences in the BLAST database %U means the number of bytes used by the BLAST database For every format each line of output will correspond to a BLAST database. Default = `%f %p' * Incompatible with: info, entry, entry_batch, outfmt, strand, target_only, ctrl_a, get_dups, pig, range, db, info, mask_sequence, line_length, show_blastdb_search_path -exact_length Get exact length for db info * Requires: info -long_seqids Use long seq id for fasta deflines * Incompatible with: info -logfile File to which the program log should be redirected