-\chapter{Advanced Jalview}
-\section{Customising Jalview}
-\subsection{Setting preferences}
-\section{The Jalview Interface}
-\subsection{Multiple views}
-\subsection{Keyboard Editing Mode}
-\section{Regions}
-\subsection{Locked Editing}
-\subsection{Alignments including hidden regions}
-\subsection{Secondary Structure predictions}
-\section{Features and Annotations}
-
-\subsection{Annotation display}
-\subsubsection{Altering annotation row height}
-\subsection{Annotation files}
-\subsection{Feature files}
-\subsection{Moving sequence associated annotation}
-\subsection{Propagating features}
-\section{Structures}
-\subsection{Working with Modeller files}
-\subsection{Using local PDB files}
-\section{Pairwise alignments}
-\r \end{document}\r
+\section{Working with DNA}
+\label{workingwithnuc}
+Jalview was originally developed for the analysis of protein sequences, but now includes some specific features for working with nucleic acid sequences and alignments. Nucleotide sequences and alignments are recognised based on the presence the nucleotide symbols [ACGT] of greater than 85\% in the sequences. Built in codon-translation tables can be used to translate ORFs into peptides for further analysis. EMBL records retrieved {\sl via} the sequence fetcher (see section \ref{fetchseq}) are also parsed in order to identify codon regions and extract peptide products.
+Furthermore, Jalview records mappings between protein sequences that are derived from regions of a nucleotide sequence. Mappings are used to to transfer annotation between nucleic acid and protein sequences, and to dynamically highlight regions in one sequence that correspond to the position of the mouse pointer in another.
+
+\subsection{Alignment and Colouring}
+
+Jalview provides a simple colourscheme for DNA bases, but does not apply any specific conservation or substitution score model for the shading of nucleotide alignments. However, pairwise alignments performed using the {\sl Alignment Window $\Rightarrow$ Calculations $\Rightarrow$ Pairwise Alignment \ldots} option will utilise an identity score matrix to calculate alignment score when alignment two nucleotide sequences.
+
+\subsubsection{Aligning Nucleic Acid Sequences}
+
+Jalview only has limited knowledge of the capabilities of the programs that are made available to it {\sl via} web services. In particular, only the ClustalW and MAFFT programs will successfuly recognise and align nucleic acid sequences. MAFFT will also choose an appropriate parameter model. Whilst Muscle may appear to align DNA, it simply treats the base symbols as amino-acids, often leading to a poor quality alignment. Furthermore, it will almost certainly fail to align RNA containing Uracil bases, since 'U' is not a valid one-letter amino acid code.
+
+\subsection{Translate cDNA}
+
+The {\sl Calculations $\Leftarrow$ Translate cDNA} function in the alignment window is only available when working with a nucleic acid alignment. It uses the standard codon translation table given in the online help to translate a nucleotide alignment, or the currently selected region, into a set of aligned peptide sequences. Any features or annotation present on the nucleotide alignment will also be translated, allowing DNA alignment analysis results to be transferred on to peptide products for further investigation.
+
+\subsection{Linked DNA and Protein Views}
+
+\parbox{3.5in}{
+Views of alignments involving DNA sequences are linked to views of alignments containing their peptide products in a similar way to views of protein sequences and views of their associated structures. Peptides translated from cDNA and extracted from EMBL records for DNA contigs are linked to their 'parent' coding regions. Mousing over a region of the peptide highlights codons in views showing the original coding region.
+}\parbox{3in}{
+\begin{center}
+%\begin{figure}[htbp]
+
+\includegraphics[width=2.8in]{images/cdnatranslinkedwin.pdf}
+
+%\caption{{\bf Linked DNA and Protein Views.} }
+%\end{figure}
+\end{center}
+}
+
+
+\subsection{Coding regions from EMBL records}
+
+Many EMBL records that can be retrieved from the sequence fetcher contain exons. Coding regions will be marked as features on the EMBL nucleotide sequence, and Uniprot database cross references will be listed in the tooltip displayed when the mouse hovers over the sequence ID. Uniprot database cross references extracted from EMBL records are sequence cross references, and associate a Uniprot sequence's coordinate system with the coding regions annotated on the EMBL sequence. Jalview utilises cross-reference information in two ways.
+\subsubsection{Retrieval of Protein or DNA Cross References}
+The {\sl Calculations $\Rightarrow$ Get Cross References } function is only available when Jalview recognises that there are protein/DNA cross-references present on sequences in the alignment. When selected, it retrieves the cross references from the alignment's dataset (a set of sequence and annotation metadata shared between alignments) or using the sequence database fetcher. This function can be used for EMBL sequences containing coding regions to open the Uniprot protein products in a new alignment window. The new alignment window that is opened to show the protein products will also allow dynamic highlighting of codon positions in the EMBL record for each residue in the product(s).
+
+\subsubsection{Retrieval of protein DAS features on coding regions}
+
+The Uniprot cross-references derived from EMBL records can be used by Jalview to visualize protein sequence features directly on nucleotide alignments. This is because the database cross references include the sequence coordinate mapping information to correspond regions on the protein sequence with that of the nucleotide contig. Jalview will use the Uniprot accessions associated with the sequence to retrieve features, and then map them onto the nucleotide sequence's coordinate system using the coding region location.
+
+\begin{figure}[htbp]
+\begin{center}
+\label{dnadasfeatures}
+\includegraphics[width=5in]{images/dnadasfeatures.pdf}
+
+\caption{Uniprot and PDB sum features retrieved {\sl via} DAS and mapped onto coding regions of EMBL record V00488}
+
+\end{center}
+\end{figure}
+
+\exercise{Visualizing protein features on coding regions}
+{
+\exstep{Use the sequence fetcher to retrieve EMBL record V00488.}
+\exstep{Ensure that {\sl View $\Rightarrow$ Show Sequence Features} is checked and change the alignment view format to Wrapped mode so the distinct exons can be seen.}
+\exstep{Open the DAS sequence feature fetcher window and fetch features for V00488 the Uniprot reference server, and any additional servers that work with the Uniprot coordinate system.}
+\exstep{Mouse over the features retrieved, note that they have been mapped onto the coding regions, and in some cases broken into several parts to cover the distinct exons.}
+\exstep{Open a new alignment view containing the Uniprot protein product with {\sl Calculations $\Rightarrow$ Get Cross References $\Rightarrow$ Uniprot } and examine the database references and sequence features. Experiment with the interactive highlighting of codon position for each residue.
+}
+}
+
+% \chapter{Advanced Jalview}
+%
+% \section{Customising Jalview}
+% \subsection{Setting preferences}
+%
+% The Jalview Desktop stores configuration and history information in a file stored in the users home directory, called '.jalview\_properties'. Many of the options stored in this file are presented in the {\sl Desktop $\Rightarrow$ Tools $\Rightarrow$ Preferences\ldots} dialog. These preferences include default settings for : {\bf Visual} layout settings for alignment views and controlling the display of the default alignment, {\bf Connection} preferences such as the standard set of URL paths that are available from the links menu and the URL which is opened when a Sequence's ID is double clicked, {\bf Editing} settings like {\sl Pad Gaps} and autocalculation of consensus, {\bf Output} settings control the degree of meta-information written in alignment files and mode of EPS figure generation, and finally the {\bf Das Settings} which allows the default DAS sources to be configured.
+%
+% \subsection{Adding your own URL links}
+%
+% \subsection{Working with Databases and Database Cross References}
+% \label{getcrossrefs}
+%
+% {\sl Calculations $\Rightarrow$ Get Cross References }
+%
+% \section{Jalview IO Interface}
+% \subsection{Multiple views}
+% \subsection{Annotation files}
+% \subsection{Feature files}
+% \subsection{Moving sequence associated annotation}
+% \subsection{Propagating features}
+% \section{Structures}
+% \subsection{Working with Modeller files}
+% \subsection{Using local PDB files}
+% \section{Pairwise alignments}
+\r \end{document}