The options listed in the table below overlap with those specified by other parameters. The initial purpose of 'OTHER_ADVANCED' is to allow users to input custom values not listed in BLAST pages. For the BLAST URLAPI, only those options not specifiable by individual parameters, given in bold, are important since they can only be used throug the 'OTHER_ADVANCED' parameter.
| Table 6.7 Option and Value for OTHER_ADVANCED | ||
| Option | Value | Function |
|---|---|---|
| -G | integer | Cost to open a gap, see GAPCOSTS (5.1.22) |
| -E | integer | Cost to extend a gap, see GAPCOSTS (5.1.22) |
| -r | integer | Reward for nucleotide match, see MATCH_SCORES (5.1.31) |
| -q | negative integer | Penalty for nucleotide mismatch, see MATCH_SCORES (5.1.31) |
| -e | double | Expect value cutoff, see EXPECT (5.1.14) |
| -W | integer | Word size, see WORD_SIZE (5.1.62) |
| -y | integer | X dropoff for blast extension in bits: 20 for nucleotide; 7 for others; megablast n/a. |
| -X | integer | X dropoff value for gapped alignment in bits: 30 for blastn and megablast; 15 for others. |
| -Z | integer | Final X dropoff value for gapped alignment in bits: 50 for blastn; 25 for others; megablast 50 |
| -P | integer | 0 for multiple hits 1-pass, 1 for single hit 1-pass not applicable to blastn/megablast. |
| -A | integer | Two hits window size |
| -I | integer | Number of database sequences to save hits for, see HITLIST_SIZE (5.1.25) |
| -b | integer | Number of database sequences to show alignments for, see ALIGNMENTS (5.1.1) |
| -v | integer | Number of database sequences to show one-line descriptions for, see DESCRIPTIONS (5.1.11) |
| -Y | real | Effective length of the search space, see SEARCHSP_EFF (5.1.53) |
| -z | real | Effective length of the database. Default zero, or actual size. |
| -c | integer | Pseudo-count constant for PSI-BLAST, default=7. |
| -F | string | Filtering directives, see FILTER (5.1.18) |
| -t | integer, 0-3 | Type of composition based statistics to apply for protein blast, see COMPOSITION_BASED_STATISTICS (5.1.6) |