Figures and Legends for Horizon Press Computational Genomics chapters by Steven M. Thompson.

Chapter 3; Multiple Sequence Alignment and Analysis, Part I, An Introduction to the Theory and Application of Multiple Sequence Analysis:

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Figure 3.1. A GCG PrettyBox multiple sequence alignment and simple motif consensus of Elongation Factor Tu/1a from several different organisms illustrates the conservation of the first of several GTP-binding domains, that region starting at position nineteen here, the P-Loop.

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Figure 3.2. A RasMac (http://openrasmol.org/) "Strands" graphic of the Giardia EF1a structural model superimposed over eight homologous chains of known structure.

Chapter 4; Multiple Sequence Alignment and Analysis, Part II, A Practical Tour of SeqLab, the Accelrys GCG Wisconsin Package Graphical User Interface:

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Figure 4.1. Protein Data Bank 1EFT: The Thermus aquaticus elongation factor Tu structure in its GTP conformation (Kjeldgaard, et al., 1993). Structural visualization by NCBI's Cn3D (http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml).

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Figure 4.2. The Wisconsin Package SeqLab LookUp window. LookUp is an SRS derivative that allows for the construction of complex, text-based sequence database queries. It produces GCG list file format output.

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Figure 4.3. The SeqLab Editor window with a LookUp dataset loaded using "Residue Coloring," ready to analyze.

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Figure 4.4. FastA can be used as a tool to sort GCG list files into ranked order based on similarity to a particular query. All or any desired portion of this output can then be loaded into the SeqLab editor for further analysis. The top portion of the example's FastA output is seen here.

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Figure 4.5. SeqLab can use 'cartoons' to graphically display the feature annotation contained in sequence database entries and produced by programs such as MotifSearch. SeqLab merges this annotation with existing datasets with the "Add to Editor" and "Overwrite" old with new function. It also allows the user to 'zoom in or out' on a dataset to see its entire length. This figure shows the unaligned dataset using "Graphic Features" and a "4:1" zoom ratio. Annotations now include the original database Feature Table entries as well as conserved elements discovered by MEME/MotifSearch.

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Figure 4.6. Motifs can create an RSF file with the location of PROSITE patterns annotated by color and shape. The display now shows annotation from the database, from Motifs, and from MEME/MotifSearch, using "Features Coloring" and a "4:1" zoom ratio.

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Figure 4.7. The PileUp program automatically plots a cluster dendrogram of the similarities between the sequences of your dataset. The lengths of the vertical lines are proportional to those similarities. This is not an evolutionary tree and should never be presented as one!

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Figure 4.8. The PileUp alignment loaded into the SeqLab Editor, displayed using "Residue Coloring."

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Figure 4.9. The PileUp aligned dataset visualized with SeqLab's "Graphic Features" annotation and a "4:1" zoom ratio. Aligned annotation now includes original database Feature Table sites, plus output from the program Motifs, and from the program pair MEME/MotifSearch.

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Figure 4.10. PlotSimilarity draws a graph of the running similarity along the length of a multiple sequence alignment using a sliding window averaging approach. Peaks are conserved regions; valleys are dissimilar areas. The ordinate scale comes from the similarity matrix used, by default the BLOSUM62 table, but the BLOSUM30 table was used here.

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Figure 4.11. PlotSimilarity can produce a color mask that can be superimposed over an open alignment in the Editor. The "Color Mask" display at a "4:1" zoom ratio now shows dark regions corresponding to conserved peaks, whereas valleys are represented with white areas.

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Figure 4.12. The t-RNA binding region of a ProfileSegments -MSF -Global alignment of selected EF-1a homologues aligned against my example 'primitive' EF-1a profile.

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Figure 4.13. EF-1a 'primitive' dataset aligned to the Thermus aquaticus EF-Tu sequence, 1EFT, by HmmerAlign. Inferred alpha helices, based on the Thermus structure, are displayed by "Features Coloring" in red. Text annotation lines have also been added to the display.

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Figure 4.14. Screen snapshot of my sample alignment showing the same region as Figure 13 but now including additional HmmerPfam annotation and displayed with "Graphic Features." Inferred alpha helices are now seen as transparent red coils.

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Figure 4.15. SeqLab "Consensus" display of a region near the carboxy termini of my EF-1a example using the BLOSUM30 matrix, a 33% "Percent required for majority" (plurality), and a cutoff value of 4 for the "Minimum score that represents" a match (threshold).

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Figure 4.16. SeqLab "Consensus" mask display of the carboxy terminal region of my EF-1a example using a weight mask generated from the BLOSUM30 matrix, a plurality of 15%, and a threshold of 4.

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Figure 4.17. SeqLab can be used to align DNA sequences against an already aligned dataset of its translational products. This is sometimes very helpful, especially when phylogenetic inference is the eventual goal.