Bioinformatics and Functional Genomics 3rd Edition

Chapter 3: Documents

This page offers the web documents that are referred to in Chapter 3 of the book, as well as various resources. In Chapter 3 we describe the pairwise alignment of two DNA or protein sequences. This is one of the most fundamental operations in bioinformatics. We discuss ways to assign scores to two aligned protein sequences. We also introduce ways to globally or locally align two sequences.

Web Document Contents
3.1 Protein sequences used to generate Fig. 3.2
3.2 Protein sequences used to generate Fig. 3.3
3.3 Amino acid composition of all proteins
3.4 GAPDH sequences used to generate Fig. 3.10
3.5 kappa casein sequences used to generate Fig. 3.11
3.6 E. coli and S. cerevisiae proteins in the FASTA format, as well as globally and locally aligned
3.7 Dotlet output: snail globin versus cytoglobin showing repeats
3.8 PRSS output for a comparison of human beta globin and myoglobin
3.9 Rat, human and bovine odorant-binding proteins and alignments
3.10 PAM10 matrix
PAM100 matrix
PAM250 matrix
PAM350 matrix