source: trunk/HELP_SOURCE/source/proteinViewer.hlp

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UP      arb.hlp
UP      glossary.hlp

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#************* Title of helpfile !! and start of real helpfile ********
TITLE           Protein Viewer 

OCCURRENCE      ARB_EDIT4/View/Protein Viewer

DESCRIPTION     Use this function to display AminoAcid sequence along with the DNA sequence.
                    
                There are six possible reading frames in every sequence, three starting at
                positions 1, 2 and 3 and going in 5'---->3' direction of a given sequence,
                and another three starting at positions 1, 2, and 3 and going in 5'--->3'
                direction of a given sequence of the complementary sequence.

                CODON TABLE:

                      Select the desired codon table from the list of standard codon
                      tables normally used in translating protein genes.

                      Refer to LINK{transl_table.hlp} for details.

                START POSITION:

                      Select the start position where the translation should begin at
                      (base position). eg., 1, 2 or 3.

                STRAND TYPE:

                      Check the "Forward Strand" to use the given sequence (as displayed)
                      for translation. And checking "Complementary Strand" uses
                      complementary sequence of the displayed sequence for translation.

                By checking "Translate from database fields" , ProteinViewer extracts
                "translation/codon table" and "start position" from the database and uses
                the same for translation.

                By default, the translated (aminoacid) sequence will be displayed as
                single letter codes. eg., A for Arginine, etc., But you can disply three
                letter aminoacid code (eg., Met for methionine) in the translated sequence
                by checking "Display Aminoacid names" checkbox.

                Display options "text" and "box" will display aminoacid codes or colored
                boxes in the translated sequence, respectively.

                Display at "Marked", "Selected", "Cursor" and "All" will toggle the display
                of aminoacid sequence only for marked, selected, cursor position and all
                species in the editor, respectively.

                SAVE AMINOACID SEQUENCE ALIGNMENT:

                      Once the alignment is refined according to the aminoacid sequence,
                      you can save the translated (aminoacid) sequence to the database as
                      a new alignment.

NOTES           This function is only visible if you are editing an DNA alignment

EXAMPLES        None

WARNINGS        None

BUGS            No bugs known