Analog of fastacmd for blast+ -bash-3.2$ /local/opt/bin/blastdbcmd -help 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 numbers] [-out output_file] [-outfmt format] [-target_only] [-get_dups] [-line_length number] [-ctrl_a] [-version] DESCRIPTION BLAST database client, 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 *** BLAST database options -db BLAST database name Default = `nr' -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 -entry_batch Input file for batch processing (Format: one entry per line) * Incompatible with: entry, pig, info -pig =0> PIG to retrieve * Incompatible with: entry, entry_batch, target_only, info -info Print BLAST database information * Incompatible with: entry, entry_batch, outfmt, strand, target_only, ctrl_a, get_dups, pig, range *** Sequence retrieval configuration options -range Range of sequence to extract (Format: start-stop) * Incompatible with: info -strand Strand of nucleotide sequence to extract Default = `plus' * Incompatible with: info -mask_sequence_with Produce lower-case masked FASTA using the algorithm IDs specified (Format: N,M,...) *** 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) %t means sequence title %l means sequence length %T means taxid %L means common taxonomic name %S means scientific name %P means PIG %mX means sequence masking data, where X is an optional comma- separted list of integers to specify the algorithm ID(s) to diaplay (or all masks if absent or invalid specification). Masking data will be displayed as a series of 'N-M' values separated by ';' or the word 'none' if none are available. For every format except '%f', each line of output will correspond to a sequence. Default = `%f' * Incompatible with: info -target_only Definition line should contain target GI only * Incompatible with: pig, info, get_dups -get_dups Retrieve duplicate accessions * Incompatible with: info, target_only *** Output configuration options for FASTA format -line_length =1> Line length for output Default = `80' -ctrl_a Use Ctrl-A as the non-redundant defline separator * Incompatible with: info