source: branches/lib/HELP_SOURCE/source/proteinViewer.hlp

Last change on this file was 19532, checked in by westram, 4 months ago
  • reintegrates 'help' into 'trunk'
    • tweak arb documentation:
      • automatically link
        • ticket references to arb bug tracker (only affects html version).
        • found URLs.
      • page titles
        • warn about long titles.
        • introduce SUBTITLEs (automatically triggered by multi-line titles in source files).
        • increase allowed length (limited by subwindow width).
      • cleanup header sections in all helpfiles.
      • fix and/or update several help files.
      • document syntax of help sources.
      • build issues:
        • when xml validation fails, next build no longer uses invalid xml ⇒ keeps failing.
        • remove output files on error (including files below ARBHOME/lib).
        • pipe output through logs to ensure proper wrapping in Entering/Leaving lines.
    • moves Tree admin + NDS menu entries to top of menu
  • adds: log:branches/help@18783:19531
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 2.6 KB
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1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4
5#       sub topics:
6#SUB     subtopic.hlp
7
8# format described in ../help.readme
9
10
11TITLE           Protein Viewer
12
13OCCURRENCE      ARB_EDIT4/View/Protein Viewer
14
15DESCRIPTION     Use this function to display AminoAcid sequence along with the DNA sequence.
16
17                There are six possible reading frames in every sequence, three starting at
18                positions 1, 2 and 3 and going in 5'---->3' direction of a given sequence,
19                and another three starting at positions 1, 2, and 3 and going in 5'--->3'
20                direction of a given sequence of the complementary sequence.
21
22                CODON TABLE:
23
24                      Select the desired codon table from the list of standard codon
25                      tables normally used in translating protein genes.
26
27                      Refer to LINK{transl_table.hlp} for details.
28
29                START POSITION:
30
31                      Select the start position where the translation should begin at
32                      (base position). eg., 1, 2 or 3.
33
34                STRAND TYPE:
35
36                      Check the "Forward Strand" to use the given sequence (as displayed)
37                      for translation. And checking "Complementary Strand" uses
38                      complementary sequence of the displayed sequence for translation.
39
40                By checking "Translate from database fields" , ProteinViewer extracts
41                "translation/codon table" and "start position" from the database and uses
42                the same for translation.
43
44                By default, the translated (aminoacid) sequence will be displayed as
45                single letter codes. eg., A for Arginine, etc., But you can disply three
46                letter aminoacid code (eg., Met for methionine) in the translated sequence
47                by checking "Display Aminoacid names" checkbox.
48
49                Display options "text" and "box" will display aminoacid codes or colored
50                boxes in the translated sequence, respectively.
51
52                Display at "Marked", "Selected", "Cursor" and "All" will toggle the display
53                of aminoacid sequence only for marked, selected, cursor position and all
54                species in the editor, respectively.
55
56                SAVE AMINOACID SEQUENCE ALIGNMENT:
57
58                      Once the alignment is refined according to the aminoacid sequence,
59                      you can save the translated (aminoacid) sequence to the database as
60                      a new alignment.
61
62NOTES           This function is only visible if you are editing an DNA alignment
63
64EXAMPLES        None
65
66WARNINGS        None
67
68BUGS            No bugs known
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