+
+\subsection{From a URL}
+Jalview can read sequence alignments directly from a URL. Please note that the
+files must be in a sequence alignment format - an HTML alignment or graphics
+file cannot be read by Jalview.
+Select {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From URL} from the
+main menu and a window will appear asking you to enter the URL (Figure
+\ref{loadurl}). Jalview will attempt to automatically discover the file format.
+
+%[fig 7]
+\begin{figure}[htbp]
+\begin{center}
+\includegraphics[width=2in]{images/menuloadurl.pdf}
+\includegraphics[width=3in]{images/loadurlbox.pdf}
+\caption{{\bf Opening an alignment from a URL. }}
+\label{loadurl}
+\end{center}
+\end{figure}
+
+\subsection{Cut and Paste}
+\label{cutpaste}
+Documents such as those produced by Microsoft Word cannot be readily understood
+by Jalview. The way to read sequences from these documents is to select the
+data from the document and copy it to the clipboard. There are two ways to
+do this. One is to right-click on the desktop background, and select the
+`Paste to new window' option in the menu that appears. The other is to select
+{\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From Textbox} from the
+main menu, paste the sequences into the text window that will appear, and select
+{\sl New Window} (Figure \ref{loadtext}). In both cases, presuming that they are
+in the right format, Jalview will happily read them into a new alignment window.
+%[fig 8]
+
+\begin{figure}[htbp]
+\begin{center}
+\includegraphics[width=2in]{images/menuloadtext.pdf}
+\includegraphics[width=3in]{images/loadtextbox.pdf}
+\caption{{\bf Opening an alignment from pasted text. }}
+\label{loadtext}
+\end{center}
+\end{figure}
+
+
+\subsection{From a Public Database}
+\label{fetchseq}
+Jalview can retrieve sequences and sequence alignments from the public databases
+housed at the European Bioinformatics Institute, including Uniprot, Pfam, Rfam
+and the PDB. Jalview's sequence fetching capabilities allow you to avoid having to
+manually locate and save sequences from a web page before loading them into
+Jalview. It also allows Jalview to gather additional metadata provided by the
+source, such as annotation and database cross-references.
+
+To begin retrieving data, select {\sl File $\Rightarrow$ Fetch Sequences \ldots}
+from the main menu. A window will then appear (Figure \ref{loadseq}) showing all
+the database sources Jalview can access (grouped by the type of database). Once
+you've selected the appropriate database by double clicking it or hitting OK, the
+database selection window will close and the sequence fetcher for that database
+will appear. You can then enter one or several database IDs or accession numbers
+separated by a semicolon and press OK. Jalview will then attempt to retrieve them
+from the chosen database. Example queries are provided for some databases to test
+that a source is operational, and can also be used as a guide for the type of
+accession numbers understood by the source.
+% [fig 9]
+\begin{figure}[htbp]
+\begin{center}
+\includegraphics[width=5in]{images/fetchseq.pdf}
+\caption{{\bf Retrieving sequences from a public database.}}
+\label{loadseq}
+\end{center}
+\end{figure}
+
+ \subsection{Memory Limits}