Tips for DB Searches

• 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.