
     map.doc                                                update 10/29/90
                                      MAP

     I. Function- MAP reads restriction site information from a file and 
     produces a file of coordinates which represent circular or linear 
     restriction maps. LINEPLOT then plots these points to form the specified 
     image. 

     II. Menus
     MAP begins by asking the user for input and output filenames.  The input
     file is usually the output from INTREST or BACHREST, listing of locations
     of restriction sites in a sequence.  The output file will be written to
     the specified file in the format required by LINEPLOT to produce a map.
     
     A. Linear Maps - Main menu
     
     Linear maps will appear on LINEPLOT output as paralell horizontal lines.
     Up to eleven lines may appear on the same map, numbered 0 to 10 going 
     from bottom to top.  Only those lines explicitly included in the map
     will appear.  The main menu below shows that the user has already 
     made maps on lines 5, 8, and 10. The top line of the menu shows the name
     and topology of the test sequence.

     Name: PEAFED1                  Topology:     LINEAR
     ______________________________________________________________________          

                          --------------------------------
                 LINE (y) |  1  2  3  4  5  6  7  8  9 10|
                          |------------------------------|
                INCLUDED? |  n  n  n  n  y  n  n  y  n  y|
                          --------------------------------
     ______________________________________________________________________          
     Map coordinates can be calculated for parallel horizontal lines.
     Type a Y coordinate between 0 and 10 (0 to quit):
     The names of enzymes with known sites in PEAFED1 
     will be displayed a screenful at a time.
     You will be asked to specify enzymes one at a time,
     to include in this map.
     There are             62 enzymes listed.
     Press RETURN to begin.

     B. Circular Maps - Main menu
     
     Circular maps will appear on LINEPLOT output as concentric circles.
     Up to ten circles may appear on the same map, numbered 1 to 10 going 
     from inside to out.  Only those circles explicitly included in the map
     will appear.  The main menu below shows that the user has already 
     made maps on circles 6, 8, and 10. The top line of the menu shows the
     name and topology of the test sequence.




     Name: PEAFED1                  Topology:   CIRCULAR
     ______________________________________________________________________          

                          --------------------------------
          CIRCLE (radius) |  1  2  3  4  5  6  7  8  9 10|
                          |------------------------------|
                INCLUDED? |  n  n  n  n  n  y  n  y  n  y|
                          --------------------------------
     ______________________________________________________________________          
     Map coordinates can be calculated for circles with different radii:
     Type a radius value between 1 and 10 (0 to quit):
     The names of enzymes with known sites in pBR322 
     will be displayed a screenful at a time.
     You will be asked to specify enzymes one at a time,
     to include in this map.
     There are             62 enzymes listed.
     Press RETURN to begin.

     C. Include menu
     For both linear and circular maps, the include menu allows the user to 
     add restriction enzymes to a map and choose the character used to 
     represent a given enzyme.  In the example shown below, we see that the 
     include menu has a top line similar to that in the main menu, with the
     exception that it also tells the Y value of the line on which the current
     map is being plotted.  For circular maps, the radius of the current
     circle would be listed instead.  

     Name: PEAFED1                  Topology:     LINEAR            Y:    8
     ______________________________________________________________________         
       1[ ]Acc1        2[ ]Alu1        3[ ]Asu2        4[ ]Ava2      
       5[ ]Ban1        6[ ]Ban2        7[ ]Ban3        8[ ]Bbv1      
       9[ ]Bcl1       10[ ]Bgl2       11[ ]Bsp1286    12[ ]BstN1     
      13[ ]Cfo1       14[ ]Cla1       15[ ]Cla2       16[ ]Dde1      
      17[ ]Dpn1       18[ ]Dra1       19[ ]EcoO109    20[ ]EcoR1*    
      21[ ]EcoR2      22[ ]EcoR5      23[ ]Fnu4H1     24[ ]Fok1      
      25[ ]Hae2       26[ ]Hae3       27[ ]Hga1       28[ ]HgiA1     
      29[ ]Hha1       30[ ]Hinc2      31[ ]Hind3      32[ ]Hinf1     
      33[ ]HinP1      34[ ]Hpa2       35[h]Hph1       36[ ]Mbo1      
      37[ ]Mbo2       38[ ]Mnl1       39[ ]Msp1       40[ ]Mst2      
      41[ ]Nci1       42[ ]Nde1       43[ ]Nde2       44[ ]Nla3      
      45[ ]Nla4       46[ ]Nsp2       47[ ]PpuM1      48[ ]Pss1      
      49[ ]Rsa1       50[ ]Sac1       51[ ]Sau3A1     52[ ]Sau96-1   
      53[ ]Sca1       54[ ]ScrF1      55[ ]SfaN1      56[ ]Spe1      
      57[ ]Sph1       58[ ]Ssp1       59[ ]Sst1       60[ ]Taq1      
      61[X]Xho2       62[ ]Xmn1      
     ______________________________________________________________________         
     Type the number of an enzyme to include in this map or 0 to continue:
     14
     Type a character to use for Cla1      
     C

     As shown above, the user has added enzyme 14, Cla1, to the map, to be
     represented by the character C.  As shown above, Xho2 and Hph1 had
     previously been added to the map, using the characters X and h, respec-
     tively. 
     
     III. Output

     The output below is a circular map of pBR322, produced by LINEPLOT using
     the output file generated by MAP.  The LINEPLOT parameters SCALES and
     AXES were set to N, since printing scales and axes would
     clutter the map.  E= EcoR1, H= Hind3 B= BamH1 and N= BstN1.
     
                                .....EH....
                             ....         ....
                           ...               ..B
                         ...                   ...
                        ..                       ..
                       ..        ......N..        ..
                      .        ...       ...        .
                     .       ..             ..       .
                    ..      ..               ..      ..
                    .      .                   .      .
                   .      ..                   ..      .
                   .     ..                     ..     .
                   .     .                       .     .
                  .      .                       .      .
                  .      .                       .      .
                  .      .                       .N     .
                  .      .                       .      .
                  .      .                       .      .
                   .     .                       .     .
                   .     ..                     ..     .
                   .      ..                   .N      .
                    .      .                   .      .
                    ..      ..               ..      ..
                     .       NN             ..       .
                      .        .N.       ...        .
                       ..        .........        ..
                        ..                       ..
                         ...                   ...
                           ...               ...
                             ....         ....
                                ...........
     
     
     
     

      Restriction map of pBR322


     IV. Input File
     MAP expects exactly the same input as DIGEST.  See the INPUT FILE 
     section of the DIGEST instructions. 

     V. Usage Notes
     1.  Remember, MAP DOES NOT DIRECTLY PRINT THE IMAGE.  It only produces 
         coordinates so that LINEPLOT can make the graph. 
     2.  As many enzymes as you wish may be included on a given map.  User 
         should make sure that no two enzymes are symbolized by the same 
         character on one map. 
     3.  The RADIUS value mentioned above refers to a fraction of the 
         graph's printing positions available.  Thus when ABCISSA is set to 
         50 char, RADIUS=5 will yeild a circle 25 char in diameter, centered 
         on the center of the graph. 
     4.  If you wish to print a circular linear maps of a circular molecules,
         make sure to indicate to BACHREST or INTREST that the molecule is
         to be considered linear. (MAP determines the topology of the
         sequence from the input file.  However, it is not always sufficient
         to change the word at the top of the file, because sites that 
         overlap the "ends" of a circular sequence would be included, unless
         the entire search was re-run by BACHREST or INTREST.)   For free
         format files, this can be done when the sequence is read in.  BIONET
         or GENBANK files must be doctored to indicate that the sequence is
         to be considered linear.
