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.