-now displayed. Close the sequence feature settings box by clicking OK or
-Cancel.} }
-
-\subsection{Creating User Defined Annotation}
-
-Annotations are properties that apply to the alignment as a whole and are visualized on rows in the annotation panel.
-To create a new annotation row, right click on the annotation label panel and select the {\sl Add New Row} menu option (Figure \ref{newannotrow}). A dialogue box appears. Enter the label to use for this row and a new row will appear.
-
-\begin{figure}[htbp]
-\begin{center}
-\includegraphics[width=1.3in]{images/annots1.pdf}
-\includegraphics[width=2in]{images/annots2.pdf}
-\caption{{\bf Creating a new annotation row.} Annotation rows can be reordered by dragging them to the desired place.}
-\label{newannotrow}
-\end{center}
-\end{figure}
-
-To create a new annotation, first select all the positions to be annotated on the appropriate row. Right-clicking on this selection brings up the context menu which allows the insertion of graphics for secondary structure ({\sl Helix} or {\sl Sheet}), text {\sl Label} and the colour in which to present the annotation (Figure \ref{newannot}). On selecting {\sl Label} a dialogue box will appear, requesting the text to place at that position. After the text is entered, the selection can be removed and the annotation becomes clearly visible\footnote{When annotating a block of positions, the text can be partly obscured by the selection highlight. Pressing the [ESC] key clears the selection and the label is then visible.}. Annotations can be coloured or deleted as desired.
-
-\begin{figure}[htbp]
-\begin{center}
-\includegraphics[width=2in]{images/annots3.pdf}
-\includegraphics[width=2in]{images/annots4.pdf}
-\includegraphics[width=2in]{images/annots5.pdf}
-\caption{{\bf Creating a new annotation.} Annotations are created from a selection on the annotation row and can be coloured as desired.}
-\label{newannot}
-\end{center}
-\end{figure}
-
-\exercise{Annotating Alignments}{
-\exstep{Load the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}.
-Right-click on the {\sl Conservation} annotation row to
-bring up the context menu and select {\sl Add New Row}. A dialogue box will appear asking for {\sl Label for annotation}.
-Enter ``Iron binding site" and click OK. A new, empty, row appears.
-}
-\exstep{
-Navigate to column 97. Move down and on the new annotation row called
-``Iron binding site, select column 97.
-Right click at this selection and select {\sl Label} from the context menu.
-Enter ``Fe" in the box and click OK. Right-click on the selection again and select {\sl Colour}.
-Choose a colour from the colour chooser dialogue
-and click OK. Press [ESC] to remove the selection.
-}
-\exstep{ Select columns 70-77 on the annotation row. Right-click and choose {\sl Sheet} from the
- context menu. You will be prompted for a label. Enter ``B" and press OK. A new line showing the
- sheet as an arrow appears. The colour of the label can be changed but not the colour of the sheet
- arrow.
-}
-\exstep{Right click on the title text of annotation row that you just created.
-Select {\sl Export Annotation} and, in the {\bf Export Annotation} dialog box that will open, select the Jalview format and click
-the [To Textbox] button.
-
-The format for this file is given in the Jalview help. Press [F1] to open it, and find
-the ``Annotations File Format'' entry in the ``Alignment Annotations'' section of the contents
-pane. }
-
-\exstep{Export the file to a text editor and edit the file to change the name of the annotation
-row. Save the file and drag it onto the alignment view.}
-\exstep{Try to add an additional helix somewhere along the row by editing the file and
-re-importing it.
-{\sl Hint: Use the {\bf Export Annotation} function to view what helix annotation looks like in
-a Jalview annotation file.}}
-\exstep{Use the {\sl Alignment Window $\Rightarrow$ File $\Rightarrow$ Export Annotations...}
-function to export all the alignment's annotation to a file.}
-\exstep{Open the exported annotation in a text editor, and use the {\bf Annotation File Format}
-documentation to modify the style of the Conservation, Consensus and Quality annotation rows so
-they appear as several lines on a single line graph.
-{\sl Hint: You need to change the style of annotation row in the first field of the annotation
-row entry in the file, and create an annotation row grouping to overlay the three quantitative
-annotation rows.}
-}
-\label{viewannotfileex}\exstep{Recover or recreate the secondary structure
-prediction that you made in exercise \ref{secstrpredex}. Use the {\sl File $\Rightarrow$ Export
-Annotation} function to view the Jnet secondary structure prediction annotation row. Note the
-{\bf SEQUENCE\_REF} statements surrounding the row specifying the sequence association for the
-annotation. } }
-
-\chapter{Multiple Sequence Alignment}
-\label{msaservices}
-Sequences can be aligned using a range of algorithms provided by JABA web
-services. These include ClustalW\footnote{{\sl ``CLUSTAL W: improving the
-sensitivity of progressive multiple sequence alignment through sequence
-weighting, position specific gap penalties and weight matrix choice."} Thompson
-JD, Higgins DG, Gibson TJ (1994) {\sl Nucleic Acids Research} {\bf 22},
-4673-80}, Muscle\footnote{{\sl ``MUSCLE: a multiple sequence alignment method
-with reduced time and space complexity"} Edgar, R.C.
-(2004) {\sl BMC Bioinformatics} {\bf 5}, 113}, MAFFT\footnote{{\sl ``MAFFT: a
-novel method for rapid multiple sequence alignment based on fast Fourier
-transform"} Katoh, K., Misawa, K., Kuma, K. and Miyata, T. (2002) {\sl Nucleic
-Acids Research} {\bf 30}, 3059-3066. and {\sl ``MAFFT version 5:
-improvement in accuracy of multiple sequence alignment"} Katoh, K., Kuma, K.,
-Toh, H. and Miyata, T. (2005) {\sl Nucleic Acids Research} {\bf 33}, 511-518.},
-ProbCons,\footnote{PROBCONS: Probabilistic Consistency-based Multiple Sequence
-Alignment.
-Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S.
-(2005) {\sl Genome Research} {\bf 15} 330-340.} T-COFFEE\footnote{T-Coffee:
-A novel method for multiple sequence alignments. (2000) Notredame, Higgins and
-Heringa {\sl JMB} {\bf 302} 205-217} and Clustal Omega.\footnote{Fast, scalable
-generation of high-quality protein multiple sequence alignments using Clustal
-Omega. Sievers F, Wilm A, Dineen DG, Gibson TJ, Karplus K, Li W, Lopez R,
-McWilliam H, Remmert M, Soding J, Thompson JD, Higgins DG (2011) {\sl Molecular
-Systems Biology} {\bf 7} 539
-\href{http://dx.doi.org/10.1038/msb.2011.75}{doi:10.1038/msb.2011.75}} Of these,
-T-COFFEE is the slowest, but also the most accurate. ClustalW is historically
-the most widely used. Muscle is faster than ClustalW and probably the most
-accurate for smaller alignments and MAFFT is probably the best for large
-alignments, however {\bf Clustal Omega}, which was released in 2011, is
-arguably the fastest and most accurate tool for protein multiple alignment.