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.
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This chapter was written by Dr. Andreas D. Baxevanis in his private capacity. No official support or endorsement by the National Institutes of Health or the United States Department of Health and Human Services is intended or should be inferred.
4 Genome Browsers
