\vspace{2in}
-Manual version 1.3
+Manual version 1.3.01
-30th November 2011
+6th December 2011
\end{center}
-\clearemptydoublepage
+\newpage
+
+% \clearemptydoublepage
% ($Revision$) 11th October 2010.}
% TODO revise for 2.6
\exercise{Retrieving features with DAS}{
\label{dasfeatretrexcercise}
-\exstep{Load the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}. Select {\sl View $\Rightarrow$ Sequence Features\ldots} from the alignment window menu. Select the {\sl DAS Settings} tab. A long list of available DAS sources is listed. Select a small number, eg Uniprot, DSSP, signalP and netoglyc. Click {\sl OK}. A window may prompt whether you wish Jalview to map the sequence IDs onto Uniprot IDs. Click {\sl Yes}. Jalview will start retrieving features. As features become available they will be mapped onto the alignment.
-}
-\exstep{If Jalview is taking too long to retrieve features, the process can be cancelled with the {\sl Cancel Fetch} button. Rolling the mouse cursor over the sequences reveals a large number of features annotated in the tool tip. Close the Feature Settings window.
-}
+\exstep{Load the alignment at
+\textsf{http://www.jalview.org/tutorial/alignment.fa}. Select {\sl View
+$\Rightarrow$ Feature Settings \ldots} from the alignment window menu. Select
+the {\sl DAS Settings} tab. A long list of available DAS sources is listed. Select a small number, eg Uniprot, DSSP, signalP and netoglyc. Click {\sl OK}. A window may prompt whether you wish Jalview to map the sequence IDs onto Uniprot IDs. Click {\sl Yes}. Jalview will start retrieving features. As features become available they will be mapped onto the alignment. } \exstep{If Jalview is taking too long to retrieve features, the process can be cancelled with the {\sl Cancel Fetch} button. Rolling the mouse cursor over the sequences reveals a large number of features annotated in the tool tip. Close the Feature Settings window. }
\exstep{Move the mouse over the sequence ID panel. Non-positional features such as literature references and protein localisation predictions are given in the tooltip, below any database cross references associated with the sequence.}
\exstep{Search through the alignment to find a feature with a link symbol next to it. Right click to bring up the alignment view popup menu, and find a corresponding entry in the {\sl Link } sub menu. }
% TODO this doesn't work ! \includegraphics[width=.3in]{images/link.pdf}
\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. The table below shows which
-alignment programs are most appropriate for nucleotide alignment.
+are made available to it {\sl via} web services, so it is up to you, the user,
+to decide which service to use when working with nucleic acid sequences. The
+table below shows which alignment programs are appropriate for nucleotide alignment.
\begin{table}{}
\centering
\begin{tabular}{|l|c|l|}
-Program& RNA support& Notes\\
+Program& NA support& Notes\\
\hline
ClustalW& Yes&\begin{minipage}[f]{3in}
Default is to autodetect nucleotide
distance metrics.
\end{minipage}
\\
+\hline
+Muscle& Yes (treat U as T)&\begin{minipage}[f]{3in}
+Default is to autodetect nucleotide
+sequences. Editable parameters include nucleotide substitution matrices and
+distance metrics.
+\end{minipage}
+\\
+\hline
+MAFFT& Yes&\begin{minipage}[f]{3in}
+Will autodetect nucleotide sequences and use a hardwired substitution model
+(all amino-acid sequence related parameters are ignored). Unknown whether
+substitution model treats Uracil specially.
+\end{minipage}
+\\
+\hline
+ProbCons& No&\begin{minipage}[f]{3in}
+ProbCons has no special support for aligning nucleotide sequences. Whilst an
+alignment will be returned, it is unlikely to be reliable.
+\end{minipage}
+\\
+\hline
+T-COFFEE& Yes&\begin{minipage}[f]{3in}
+Sequence type is automatically detected and an appropriate
+parameter set used as required. A range of nucleotide specific
+score models are available.\end{minipage}
+\\
\end{tabular}
-\caption{JABAWS Alignment programs suitable for aligning nucleic acid
-sequences.}
+\caption{{\bf JABAWS Alignment programs suitable for aligning nucleic acid
+sequences.} All JABAWS alignment services will return an alignment if provided
+with RNA or DNA sequences, with varying reliability. No programs include
+support for taking RNA secondary structure prediction into account when
+aligning sequences.}
\label{nucleomsatools}
\end{table}
-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 $\Rightarrow$ Translate cDNA} function in the alignment
git://source.jalview.org / jalview-manual.git / blobdiff