| -show | Show all DNA and protein sequences after other operations. |
| -Mass | Show the calculated mass for each sequence. |
| -complement | Complement all DNA sequences before other operations. |
| -translate 1 | Translate all DNA sequences with this frame (0,1,2). |
| -finddna ggattcga | DNA sequence to look for in DNA sequences. |
| -findprotein fghwereaas | Protein sequence to look for in protein sequences. |
| -findcoding aklsdrtv | Coding sequence to look for in DNA sequences. |
| Can be a file name with a protein sequence. | |
| -verbose 7 | Verbosity of output. |
| -nogaps | Strip gaps from input sequences. |
| -length 1100,1500 | Sequence length range to select for. |
| -number 10,14 | Number of residues on either side to include in output. |
| -threshold 50 | Threshold percentage to report hits (default only best hit). |
| -geneticcode file.star | Genetic code file (default = internal values). |
| -elements prop.star | Calculate elemental composition. |