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<head>
<title>Alignment Window Menus</title>
</head>
When selected, these numbers are parsed into sequence associated
annotation which can then be used to sort the alignment via the Sort
by→Score menu.</em> <br></li>
-
+ <li><strong>Translate as cDNA</strong> (not applet)<br><em>This option is visible for nucleotide alignments.
+ Selecting this option shows the DNA's calculated protein product in a new window. Note that the
+ translation is not frame- or intron-aware; it simply translates all codons in each sequence, using the
+ standard <a href="../misc/geneticCode.html">genetic code</a> (any incomplete final codon is discarded).
+ You can perform this action on the whole alignment,
+ or selected rows, columns, or regions.</em> <br></li>
+ <li><strong>Get Cross-References</strong> (not applet)<br><em>This option is visible where sequences have cross-references to
+ other standard databases; for example, an EMBL entry may have cross-references to one or more UNIPROT entries.
+ Select the database to view all cross-referenced sequences in a new window.</em> <br></li>
<li><strong>Autocalculate Consensus</strong><br> <em>For
large alignments it can be useful to deselect "Autocalculate
Consensus" when editing. This prevents the sometimes lengthy