Protein-map

PEPMAP is a specialised display module in acedb, comparable to the FMAP (the display module for DNA sequence) or GMAP (the display module for genetic and other types of maps). The key sections of models that it uses are the following: 


?Protein  Title UNIQUE ?Text
          Peptide UNIQUE ?Peptide UNIQUE Int UNIQUE Int // Int Int are length, checksum
          View_info View ?View
                    Default_view UNIQUE ?View
          Homol DNA_homol ?Sequence XREF Pep_homol ?Method Float Int UNIQUE Int Int
UNIQUE Int #Homol_info
                Pep_homol ?Protein XREF Pep_homol ?Method Float Int UNIQUE Int Int UNIQUE
Int #Homol_info
                Motif_homol ?Motif XREF Pep_homol ?Method Float Int UNIQUE Int Int UNIQUE
Int #Homol_info
            // Float Int Int Int Int are score, start end in protein, start end in target
          Feature ?Method Int Int UNIQUE Float  // display according to method
            // Int Int Float are start, end, score
with reciprocal entries in ?Sequence, ?Motif for homology information.

?Peptide is an array class. You should enter protein sequence as follows: 


Peptide WP:K04C2.3
MATQTAVTATTVPQGSPSVTGSASQGGILNSARQFFSLAAPKVEKDKEFSFRFLTSP
LRSKPAATVNADNFYMYACGSINMP
similar to the way DNA is entered. This will automatically create the Protein class object with the same name, and enter the link to the peptide with the length and checksum.

The main way to enter annotation for the protein sequence is via Homol and Feature lines, exactly as for DNA. The way they are displayed are controlled by the Method object, with a different method for each different type of Match/Feature. The relevant parts of the ?Method model are: 


?Method Remark ?Text
          // the Display information controls how the column looks.
        Display Colour #Colour
                Score   Score_by_offset // has priority over width, for Jean
                        Score_by_width
                        Score_bounds UNIQUE Float UNIQUE Float 
                                // limits for squashing
                Bumpable          // bump to avoid overlap
        Blixem_P
        Belvu

The PEPMAP display uses the same system of columns controlled by a View object as the GMAP display. The relevant parts of the View models are given below, but although you need them you don't really need to understand them - they are all handled by the code and you should not enter data for them directly. 


?View   Type    UNIQUE  Pepmap
        Display Submenus        // BOOL for submenus on item boxes
                No_buttons      // suppress header buttons for WWW 
                Hide_header     // No headers and footers 
        Name    UNIQUE  Text
        Columns Text UNIQUE Int #Column // Int is BOOL for Hidden/Visible

?Column UNIQUE  Scale Scale_unit UNIQUE Float   // minimum increment
                      Cursor Cursor_on
                             Cursor_unit UNIQUE Float
                Locator Magnification UNIQUE Float
                        Projection_lines_on
                pepSequence     PS_Highlight_residue   // il all needed for colomn display of peptides
                                PS_Residues_per_wrap Int
                                PS_Colours Text #Colour
                Hydrophobicity  HP_Show_Zero_bar
                                HP_Fixed_Scaling
                                HP_Calculation_window Int
                                HP_Display_width Int
                Homol           HOM_bump
                pepFeature      FEA_bump
                                FEA_Query Text
                Homol_Name      HOM_NAME_bump
                                HOM_NAME_width Int
                pepActiveZone
there are other column types and parts of the ?View module needed for other displays. The list of columns shows what sort of information can be shown in the PEPMAP. A default View is constructed automatically, but quite a lot is configurable, and configurations can be stored as named View objects, and proteins can have default and alternative views. e.g. the sequence itself can be displayed with different colouring schemes, configurable from the view control window obtained by pressing the "View" button on the peptide display.

It looks like by default there are columns for BlastP, BlastX, Pfam-hmmls and Pfam-hmmfs. Anything other methods need adding explicitly to the View in the View control window. You can display multiple methods in one column by separating the method names with '+', e.g. "Pfam-hmmls+Pfam-hmmfs". This is all a bit hard-wired for our priorities, sorry.

Also, the PEPMAP has not been continuously developed and upgraded over the last few years, so is lacking gif drawing support for gifaceserver and new Method/Column options available in FMAP. But it is functional and quite powerful/flexible for displaying new sorts of data.

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