Normally, the table is sorted by position first and then alphabetically by enzyme name. You can sort the table by enzyme name first and then by position with Order table of cut sites by.
If you display the cut positions in a table using Write a table of cut sites (instead of restriction map), the program does not create the standard output file displaying the sequence and the restriction sites along that sequence.
POTENTIAL RESTRICTION SITES
To assist scientists doing site-directed mutagenesis, this program searches for places in your sequence where a restriction enzyme recognition site occurs with one or more mismatches. Use Number of allowed mismatches set to 1 to identify positions where recognition could occur with one or fewer mismatches.
Use Find translationally silent potential restriction sites to find the places in your sequence where a restriction site could be introduced without changing the translation. Read more about using Find translationally silent potential restriction sites under the PARAMETER REFERENCE topic below.
SEARCH FOR ANY SEQUENCE PATTERN
By changing the enzyme data file (see the LOCAL DATA FILES topic below), you can make this program search for any pattern. See Appendix VII for notes on enzyme data files.
DEFINING PATTERNS
FindPatterns, Map, MapSort, MapPlot, and Motifs all let you search with ambiguous expressions that match many different sequences. The expressions can include any legal GCG sequence character (see Appendix III). The expressions can also include several non-sequence characters, which are used to specify OR matching, NOT matching, begin and end constraints, and repeat counts. For instance, the expression TAATA(N){20,30}ATG means TAATA, followed by 20 to 30 of any base, followed by ATG. Following is an explanation of the syntax for pattern specification.
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Implied Sets and Repeat Counts
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Parentheses () enclose one or more symbols that can be repeated some number of times. Braces {} enclose numbers that tell how many times the symbols within the preceding parentheses must be found.
Sometimes, you can leave out part of an expression. If braces appear without preceding parentheses, the numbers in the braces define the number of repeats for the immediately preceding symbol. One or both of the numbers within the braces may be missing. For instance, both the pattern GATG{2,}A and the pattern GATG{2}A mean GAT, followed by G repeated from 2 to 350,000 times, followed by A; the pattern GATG{}A means GAT, followed by G repeated from 0 to 350,000 times, followed by A; the pattern GAT(TG){,2}A means GAT, followed by TG repeated from 0 to 2 times, followed by A; the pattern GAT(TG){2,2}A means GAT, followed by TG repeated exactly 2 times, followed by A. (If the pattern in the parentheses is an OR expression (see below), it cannot be repeated more than 2,000 times.)
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OR Matching
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If you are searching nucleic acids, the ambiguity symbols defined in Appendix III let you define any combination of G, A, T, or C. If you are searching proteins, you can specify any of several symbol choices by enclosing the different choices in parentheses and separating the choices with commas. For instance, RGF(Q,A)S means RGF followed by either Q or A followed by S. The length of each choice need not be the same, and there can be up to 31 different choices within each set of parentheses. The pattern GAT(TG,T,G){1,4}A means GAT followed by any combination of TG, T, or G from 1 to 4 times followed by A. The sequence GATTGGA matches this pattern. There can be several parentheses in a pattern, but parentheses cannot be nested.
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NOT Matching
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The pattern GC~CAT means GC, followed by any symbol except C, followed by AT. The pattern GC~(A,T)CC means GC, followed by any symbol except A or T, followed by CC.
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Begin and End Constraints
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The pattern <GACCAT can only be found if it occurs at the beginning of the sequence range being searched. Likewise, the pattern GACCAT> would only be found if it occurs at the end of the sequence range.
ACKNOWLEDGEMENT
We are grateful to Frank Manion for suggestions and for code used in the revision of Map for version 9.0. The vertical enzyme output format of Map was designed by John Schroeder and Frederick Blattner (NAR 10; 69-84 (1982), Figure 1). Map was written for the first release of the Wisconsin Package(TM) by Paul Haeberli and John Devereux.
PARAMETER REFERENCE
You can set the parameters listed below from the command line. For more information, see "Using Program Parameters" in Chapter 3, Using Programs in the User's Guide.
The Minimum number of cuts, Maximum number of cuts, Show enzymes that cut only once, and Suppress enzymes that cut within the region base1,base2 parameters suppress the display of selected enzymes. The list of excluded enzymes in the program output includes both selected enzymes that cut within excluded ranges and selected enzymes that did not cut the right number of times.
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Minimum number of cuts
excludes enzymes that do not cut at least the specified number of times.
Maximum number of cuts
excludes enzymes that cut more than the specified number of times.
Show enzymes that cut only once
excludes, from the set of enzymes displayed, those enzymes that cut your sequence more than once (equivalent to setting both mincuts and maxcuts to one).
Suppress enzymes that cut within the region base1,base2
excludes enzymes that cut anywhere within one or more ranges of the sequence. If an enzyme is found within an excluded range, then the enzyme is not displayed. The list of excluded enzymes includes enzymes that cut within excluded ranges. The ranges are defined with sets of two numbers. The numbers are separated by commas. Spaces between numbers are not allowed. The numbers must be integers that fall within the sequence beginning and ending points you have chosen. The range may be circular if circular mapping is being done. Exclusion is not done if there are any non-numeric characters in the numbers or numbers out of range or if there is an odd number of integers following the parameter.
Display both forward and reverse strand cut positions
shows where each enzyme cuts the reverse strand as well as the forward strand. The cut point on the bottom strand is the 5' end of the fragment which continues to the left.