X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fmenus%2Falwcalculate.html;h=50bb37b0f6489f22a53c546140298110c3cb56af;hb=0943de76f6a7435894e72479671642c05f2f3687;hp=93652aff2e1934d2434a804c12f261c662bb26b6;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git diff --git a/help/html/menus/alwcalculate.html b/help/html/menus/alwcalculate.html index 93652af..50bb37b 100755 --- a/help/html/menus/alwcalculate.html +++ b/help/html/menus/alwcalculate.html @@ -1,22 +1,24 @@ + --> Alignment Window Menus @@ -80,7 +82,15 @@ 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.
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  • Translate as cDNA (not applet)
    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 genetic code (any incomplete final codon is discarded). + You can perform this action on the whole alignment, + or selected rows, columns, or regions.
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  • Get Cross-References (not applet)
    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.
  • Autocalculate Consensus
    For large alignments it can be useful to deselect "Autocalculate Consensus" when editing. This prevents the sometimes lengthy