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1 Altschul, S.F., Boguski, M.S., Gish, W., and Wootton, J.C. (1994). Issues in searching molecular sequence databases. Nat. Genet. 6: 119–129. A review of the issues that are of importance in using sequence similarity search programs, including potential pitfalls.

2 Fitch, W. (2000). Homology: a personal view on some of the problems. Trends Genet. 16: 227–231. A classic treatise on the importance of using precise terminology when describing the relationships between biological sequences.

3 Henikoff, S. and Henikoff, J.G. (2000). Amino acid substitution matrices. Adv. Protein Chem. 54: 73–97. A comprehensive review covering the factors critical to the construction of protein scoring matrices.

4 Koonin, E. (2005. Orthologs, paralogs, and evolutionary genomics). Annu. Rev. Genet. 39: 309–338. An in-depth explanation of orthologs, paralogs, and their subtypes, with a discussion of their evolutionary origin and strategies for their detection.

5 Pearson, W.R. (2016). Finding protein and nucleotide similarities with FASTA. Curr. Protoc. Bioinf. 53: 3.9.1–3.9.23. An in-depth discussion of the FASTA algorithm, including worked examples and additional information regarding run options and use scenarios.

6 Wheeler, D.G. (2003). Selecting the right protein scoring matrix. Curr. Protoc. Bioinf. 1: 3.5.1–3.5.6. A discussion of PAM, BLOSUM, and specialized scoring matrices, with guidance regarding the proper choice of matrices for particular types of protein-based analyses.