| Program |
Query Sequence |
Database Sequences |
Comments |
| BLASTN |
Nucleotide, both strands |
Nucleotide |
- Parameters optimized for speed, not sensitivity.
- Not intended for finding distantly-related coding sequences.
- Automatically checks for complementary strand of query.
- Low-complexity filter option (dust)
|
| BLASTX |
Nucleotide, six-frame translation |
Protein |
- Very useful for preliminary data containing potential frameshift errors,
i.e., ESTs and other "single-pass" sequences.
- 12 different genetic codes available.
- 65 different scoring matrices available.
- Low-complexity filter options with SEG or XNU algorithms (highly recommended).
|
| TBLASTX |
Nucleotide, six-frame translation |
Nucleotide, six-frame translation |
- Very useful for preliminary data containing potential frameshift errors,
i.e., ESTs and other "single-pass" sequences.
- 12 different genetic codes available.
- 65 different scoring matrices available.
- Low-complexity filter options with SEG or XNU algorithms (highly recommended).
|
| BLASTP |
Protein |
Protein |
- 65 different scoring matrices available.
- Low-complexity filter options.
|
| TBLASTN |
Protein |
Nucleotide, six-frame translation |
- Essential for searching protein queries against EST database.
- Often useful for finding undocumented open reading frames or frameshift
errors in database sequences.
- Same genetic code and scoring matrix options as BLASTX.
- Low-complexity filter options (highly recommended).
|