Gap penalties that give local alignments should be used 2. make sure that correct statistical procedures are used - fasta3, ssearch and blast2 are all satisfactory 3. for finding related sequences, especially protein families, some members may not be found because the similarity is too low. Use several members of a family in database searches to reach them all 4. Agarwal P, States DJ 1998 Comparative accuracy of methods for protein sequence similarity search. Amino acid substitution matrices from an information theoretic perspective. A protein alignment scoring system sensitive at all evolutionary distances.
Protein database searches for multiple alignments.
Basic local alignment search tool. Identification of protein coding regions by database similarity search. Amino acid substitution matrices from protein blocks. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Pearson WR 1995 Comparison of methods for searching protein sequence databases.