To get a full profile for a particular gene: python hsp70-motif-finder.py --database scer_orf_trans_all.fasta --pssm rudiger --threshold 5.0 --id YAL005C --report --out ssa1-motifs.txt
(You can use --pssm vandurme to use the van Durme 2009 paper's scoring matrix.)
To get short profiles for all genes in a FASTA file: python hsp70-motif-finder.py --database scer_orf_trans_all.fasta --pssm rudiger --report --threshold 5.0 --out scer-hsp70-motifs-summary.txt
To profile a sequence you just made up: python hsp70-motif-finder.py --sequence RYLLKNRANSSTSS --pssm rudiger --threshold 5.0 --report
To mask an alignment you pass in, covering up all sites that are not scored as the center of an Hsp70 binding motif: python hsp70-motif-finder.py --database hsf-all-manual.fa --pssm rudiger --mask --threshold 5.0 --out hsf-masked-hsp70-binding-sites.fa
To get some information about these options: python hsp70-motif-finder.py --help