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<html>
<head>
<meta name="keywords" content="java, biology, bioinformatics, EMBOSS, GUI, Jemboss, computational biology, sequence analysis, interface">
<title>Jemboss Sequence List</title>
</head>
<body text="#000000" bgcolor="#FFFFFF" link="#0000EE" vlink="#551A8B" alink="#FF0000">
<center><img SRC="../images/Jemboss_logo_large.gif" height=110 width=240><br>
<h1>Sequence List</h1></center>
<p>This window allows users to store their commonly
used sequences. A sequence file can be dragged from the
file managers into this window or a database entry
(e.g. sw:pax6_human) can simply be typed into the table.
The files then can be dragged and dropped back into
the program sequence fields in the main Jemboss window
when required.
<p>An EMBOSS list file contains "references" to sequences,
for example the file could look like:
<br><tt>opsd_abyko.fasta
<br>sw:opsd_xenla
<br>sw:opsd_c*
<br>@another_list</tt>
<p>Selecting <b>'List'</b> in the Sequence List table will
automatically prepend the filename with '@' (indicating
to EMBOSS that this is a list file) when it is
dragged into a application sequence field.
<p>If the <b>'Default'</b> column is selected then this
sequence will automatically be the input sequence used
when an EMBOSS application is chosen.
<p>The sequence length can be calculated by selecting
the sequence and clicking on 'Calculate sequence attributes'
under the 'Tools' menu. The sequence start and end positions
will then be displayed.
<p><b>Saving the sequence list</b>, between Jemboss sessions,
is not done automatically.
Go to the tools menu and select 'Save Sequence List' if
this table is to be used in the next Jemboss session. This
simply creates '.jembossSeqList' file in the user's home
directory. This will then be loaded in (unless deleted
from the file system) on the next Jemboss launch.
<p>A sequence file can be <b>opened</b> by selecting the
sequence in the table and opening it from the <b>'File'</b> menu.
Extra rows can be added to the table and sequences can
be deleted from the <b>'Tools'</b> menu.
<br>
<p>
<hr>
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