Running :command:`prody blast -h` displays:
usage: prody blast [-h] [--quiet] [--examples] [-i FLOAT] [-o FLOAT] [-d PATH] [-z] [-f STR] [-e FLOAT] [-l INT] [-s INT] [-t INT] sequence positional arguments: sequence sequence or file in fasta format optional arguments: -h, --help show this help message and exit --quiet suppress info messages to stderr --examples show usage examples and exit -i FLOAT, --identity FLOAT percent sequence identity (default: 90.0) -o FLOAT, --overlap FLOAT percent sequence overlap (default: 90.0) -d PATH, --output-dir PATH download uncompressed PDB files to given directory -z, --gzip write compressed PDB file Blast Parameters: -f STR, --filename STR a filename to save the results in XML format -e FLOAT, --expect FLOAT blast search parameter -l INT, --hit-list-size INT blast search parameter -s INT, --sleep-time INT how long to wait to reconnect for results (sleep time is doubled when results are not ready) -t INT, --timeout INT when to give up waiting for results
Running :command:`prody blast --examples` displays:
Blast search PDB for the first sequence in a fasta file: $ prody blast seq.fasta -i 70 Blast search PDB for the sequence argument: $ prody blast MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG Blast search PDB for avidin structures, download files, and align all files onto the 2avi structure: $ prody blast -d . ARKCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFT $ prody align 2avi.pdb *pdb