| Typea | Element | Description |
|---|---|---|
| Nlm_FloatHi | expect_value | Expect value cutoff |
| Int2 | wordsize | Number of letters used in making words for lookup table |
| Int2 | penalty | Mismatch penalty (only blastn and MegaBLAST) |
| Int2 | reward | Match reward (only blastn and MegaBLAST) |
| CharPtr | matrix | Matrix used for comparison (not blastn or MegaBLAST) |
| Int4 | gap_open | Cost for gap existence |
| Int4 | gap_extend | Cost to extend a gap one more letter (including first) |
| CharPtr | filter_string | Filtering options (e.g., L, mL) |
| Int4 | hitlist_size | Number of database sequences to save hits for |
| Int2 | number_of_cpus | Number of CPUs to use |
The types are given in terms of those in the NCBI Toolkit. Nlm_FloatHi is a double, Int2/Int4 are 2- or 4-byte integers, and CharPtr is just char*.
From: Chapter 16, The BLAST Sequence Analysis Tool
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