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- Use latest database version
- Run BLAST first, then depending on your results run a finer tool (FastA, Ssearch, SW, Blocks, etc..)
- Whenever possible, use the translated sequence.
- E < 0.05 is statistically significant, usually biologically interesting. Check also
0.05 < E < 10 because you might find interesting hits.
- Pay attention to abnormal composition of the query sequence, since it usually causes biased scoring.
- Split large query sequences (> 1000 for DNA, > 200 for protein).
- If the query has repeated segments, remove them and repeat the search.
Peer Itsik
2000-12-11