1. Chapter 3 Gene Alignments: Investigating Antibiotic Resistance

2. Figure 3.1: Agricultural use of antibiotics: a controversial topic with major medical consequences Cows: Courtesy of Scott Bauer/USDA ARS; pills: © AbleStock

3. Figure 3.2: Vertical and horizontal gene transfer

4. Figure 3.3: How exposure to antibiotics selects for the survival of resistant cells in a population of bacteria

5. Figure 3.4: A plasmid carrying an antibiotic-resistance gene can be transferred to a new cell by conjugation

6. Figure 3.5: Determining the similarity of two or more genes by aligning their nucleotide sequences as well as possible; the differences due to mutation are shown in boxes

7. Figure 3.6a: Sample results of a BLAST search for database sequences matching a nucleotide query sequence: (A) graphical summary of results

8. Figure 3.6b: Sample results of a BLAST search for database sequences matching a nucleotide query sequence: (B) table of scores

9. Figure 3.6c: Sample results of a BLAST search for database sequences matching a nucleotide query sequence: (C) alignments

10. Figure 3.7: Sample output from a ClustalW multiple sequence alignment

11. Figure 3.8: Completed scoring matrix showing three possible alignment paths

12. Figure 3.T1: Example of a Perl array named @numbers having six elements (numbered 0 through 5) with values as shown

13. Figure 3.9: A local alignment will allow us to find the similarity in two sequences that are not similar along their entire length