prody blast

Usage

Running 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

Examples

Running 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