Rfindpatterns

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RFINDPATTERNS

RFINDPATTERNS

FUNCTION

RFindPatterns identifies sequences that contain short patterns like GAATTC or YRYRYRYR. You can define the patterns ambiguously and allow mismatches. You can provide the patterns in a file or simply type them in from the terminal. The output is a series of files called r1.rfind, r2.rfind, and so on, each containing a single extracted sequence. These can be fed through Pileup or manipulated in other ways.

DESCRIPTION

RFindPatterns locates short sequence patterns. If you are trying to find a pattern in a sequence or if you know of a sequence that you think occurs somewhere within a larger one, you can find your place with RFindPatterns RFindPatterns can look through large data sets for any short sequence patterns you specify. RFindPatterns can recognize patterns with some symbols mismatched but not with gaps. It supports the IUB-IUPAC nucleotide ambiguity codes (see Appendix III) for searching through nucleotide sequences.

RFindPatterns searches both strands of a nucleotide sequence if the patterns you specify are not identical on both strands. If your sequence is a peptide, RFindPatterns searches for a simple symbol match between your pattern and the peptide sequence.

RFindPatterns names each file on the screen as it is searched. The output file shows only sequences where a pattern was found unless you use the command-line option -SHOw. Five symbols from the original sequence are shown on either side of each "find." The word /Rev occurs if the reverse of the pattern is found. If you run RFindPatterns with the command-line option -NAMes, the output file is written in list file (formerly called file of sequence names) format, which you can use as input to other Wisconsin Sequence Analysis Package(TM) programs that support indirect file specifications

When FindPatterns finishes searching for your patterns, it returns to the first prompt in the program, RFINDPATTERNS in what sequence(s) ? If you simply press at the prompt, RFindPatterns stops.

RFindPatterns keeps writing its results in the same output file (or on the screen). RFindPatterns prints a short summary on your screen and in the output file when the entire session is over.

AUTHOR

This GCG program was modified by David Mathog (E-mail: MATHOG@seqaxp.bio.caltech.edu Post: Sequence Analysis Facility, Biology Division, Caltech), and modified for EGCG by Peter Rice (E-mail: pmr@sanger.ac.uk Post: Informatics Division, The Sanger Centre, Hinxton Hall, Cambridge, CB10 1RQ, UK).

All EGCG programs are supported by the EGCG Support Team, who can be contacted by E-mail (egcg@embnet.org).

EXAMPLE

Here is a session using RFindPatterns to determine if there are any EcoRI or BamHI sites in the human immunoglobulin sequences of the EML database (The program Fetch was used first to make a copy of the file pattern.dat):

  
  
  % rfindpatterns
  
   RFINDPATTERNS uses any sequences
  
   RFINDPATTERNS of what sequence(s) ?  GenEmbl:Hsig*
  
   Search patterns read from "pattern.dat"
  
   What should I call the output file (* rfindpatterns.rfind *) ?
  
         HUMIG22L len:        180
       HUMIGACHSR len:      3,326
        HUMIGAHA2 len:        789
  
       //////////////////////////
  
        HUMIGXJAA len:         69
        HUMIGXJAB len:         69
        HUMIGXPSA len:        237
  
   RFINDPATTERNS of what sequence(s) ?
  
  Total finds:        523
 Total length:    647,962
   Total sequences:      1,323
     CPU time:   03:18.97
  
 Output file: rfindpatterns.rfind
  
  %

OUTPUT

Here is some of the output file:

  
  
  RFINDPATTERNS on:       EM_NEW:HSIGH344P
  Original file info: M99673 Human immunoglobulin heavy chain
  variable region V3-4 4P (IGHV@) gene, exons 1-2. 8/95
  Matching pattern:  TAATA(N){20,30}ATG
  Pattern location:  114 to 151
  Lwidth: 5
  Rwidth: 5
  Match and extraction from the REVERSE strand.
  
r1  Length: 48  September 25, 1995 16:46  Type: N  Check: 5227  ..
  
    1  TTCTCTAATA TCCACTCACA AACAATATCT GTAGTTCTTC ATGAATCA

If the pattern is a complex expression, it will be written above each find along with a simplification of the pattern so that you can see what was actually found. In the above example, the Promoter pattern CAT(N){20,30}TATTA is the pattern being searched, and CATN{29}TATTA is the pattern actually found. Five symbols from the original sequence are shown on either side of the find. In the example above, 104 is the coordinate of the first C in CATCGGG ... not of the G of the flanking symbols GTCCC.

RELATED PROGRAMS

The GCG mapping programs Map, MapPlot and MapSort can be used to mark finds in the context of a DNA restriction map. Motifs looks for sequence motifs by searching through proteins for the patterns defined in the PROSITE Dictionary of Protein Sites and Patterns. FindPatterns is the original GCG version of this program, with fixed reporting of 5 flanking residues. These programs all use the same search algorithm and input data file format as RFindPatterns

RESTRICTIONS

Patterns typed in from the terminal may not be longer than 132 characters. Patterns from a data file may not be longer than 350 characters.

RFindPatterns can search for a maximum of 5,000 patterns in a nucleotide sequence. If your pattern.dat file contains more than 5,000 patterns, only the first 5,000 are used.

The restrictions specified with the -MINCuts and -MAXCuts command-line options must be fulfilled on a single strand of a nucleotide sequence in order for the find to be reported. For instance, if you use the command % rfindpatterns -MINCuts= 2 -PATterns=CCCC with the sequence CCCCGGGG, no finds will be reported, even though there is one instance of the pattern on each strand.

LIST REFINEMENT

The database programs Names, StringSearch, FindPatterns, FastA, TFastA, and WordSearch can be used for list refinement if you are looking for sequences with something in common. For instance, you could identify human globin sequences with StringSearch. The output list could then be refined with FindPatterns to show only those globin sequences containing EcoRI sites. You could then use WordSearch to compare this output list to a sequence of your own that you think is similar to these human, globin, EcoRI-containing sequences.

Adding Lists Together

You can add two lists together by simply appending one of the files to the other. It is better if you use a text editor to modify the heading of the combined list so that the annotation in the list correctly reflects what you have done. Remember to delete the text heading from the second file so that it does not occur in the middle of the list.

Suppressing Items

Suppress any item in a list by typing an exclamation point (!) in front of the item. You can also put comments into a list anywhere on a line by placing an exclamation point before the comment.

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.

Implied Sets and Repeat Counts

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, the pattern GATG{2,}A means 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. (If the pattern in the parentheses is an OR expression (see below), it cannot be repeated more than 2,000 times.)

OR Matching

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 choices 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.

NOT Matching

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.

Begin and End Constraints

The pattern would only be found if it occurs at the end of the sequence range.

CONSIDERATIONS

RFindPatterns will not introduce gaps but it can tolerate mismatches when it is run with the command-line option -MISmatch. Mismatched finds are shown in the output in lowercase.

If you are entering patterns from the command line with the -PATterns qualifier, any pattern containing a comma must be enclosed in double quotes; otherwise, the comma is assumed to separate different patterns on the command line.

SPECIFYING SEQUENCES

There is information on specifying sets of sequences in Chapter 2, Using Sequences of the User's Guide.

LARGE DATA SETS

FindPatterns is one of the few programs in GCG or EGCG that can take more than a few minutes to run. Large searches should probably be run in the batch queue. You can run this program in the batch queue on many computers by using the command-line option -BATch. Run this way, the program prompts you for all the required parameters and then automatically submits itself to the batch or at queue. Batch jobs free your terminal for other work and may allow the system manager to distribute the load on your computer more evenly. For more information, see "Using the Batch Queue" in Chapter 3, Basic Concepts: Using Programs in the User's Guide. Very large comparisons may exceed the CPU limit set by some systems.

Patterns that start with complicated OR or NOT expressions take longer to search than simple expressions like GATTC.

INPUT FILE

You can put any patterns you want to search for into a file like the one below. The pattern data files for RFindPatterns are modeled on the enzyme data files for the mapping programs described in the Data Files manual. The names should not have more than eight letters. The offset field is ignored by RFindPatterns but the field should have a number in it to make these files compatible with the files that are read by mapping programs.

The exact column used for each field does not matter, only the order of the fields in the line. You can give several patterns the same name, but put all of the entries for that name on adjacent lines of the file. The patterns may not be more than 350 characters long. Blank lines and lines that start with an exclamation point (!) are ignored.

If the overhang field is a period (.) instead of a number, only the top strand of a nucleic acid sequence is searched for the pattern. Any number implies that both strands are to be searched. The value of the overhang number has no significance to RFindPatterns Here is the pattern data file used in the example above:

  
  
  An example of a pattern data file for the program FINDPATTERNS.
  
  Name    Offset  Pattern             Overhang  Documentation  ..
  
  BamHI        1  GGATCC                     0  !
  EcoRI        1  GAATTC                     0  !
  Promotor     1  TAATA(N){20,30}ATG         0  !

SEQUENCE TYPE

The function of RFindPatterns depends on whether your input sequence(s) are protein or nucleotide. Programs determine the type of a sequence by the presence of either Type: N or Type: P on the last line of the text heading just above the sequence. If your sequence(s) are not the correct type, turn to Appendix VI for information on how to change or set the type of a sequence.

COMMAND-LINE SUMMARY

All parameters for this program may be put on the command line. Use the option -CHEck to see the summary below and to have a chance to add things to the command line before the program executes. In the summary below, the capitalized letters in the qualifier names are the letters that you must type in order to use the parameter. Square brackets ([ and ]) enclose qualifiers or parameter values that are optional. For more information, see "Using Program Parameters" in Chapter 3, Basic Concepts: Using Programs in the GCG User's Guide.

  
  
  Minimal Syntax:  rfindpatterns [^
  
  Prompted Parameters:
  
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  Local Data Files:
  
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  Optional Parameters:
  
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             *N means fills whatever size the match is with N.
             "+" means use original sequence at that position.
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  -d1.seq, temp/d2.seq and so on
  
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LOCAL DATA FILES

The files described below supply auxiliary data to this program. The program automatically reads them from a public data directory unless you either 1) have a data file with exactly the same name in your current working directory; or 2) name a file on the command line with an expression like -DATa1=myfile.dat. For more information see Chapter 4, Using Data Files in the User's Guide.

RFindPatterns can read the patterns you want to find from the file pattern.dat in your working directory. If you don't have a file called pattern.dat in your directory, RFindPatterns asks you to type in the patterns you want to find. If you want to use a pattern data file with a name other than pattern.dat, include -DATa=filename on the command line.

OPTIONAL PARAMETERS

The parameters and switches listed below can be set from the command line. For more information, see "Using Program Parameters" in Chapter 3, Basic Concepts: Using Programs in the GCG User's Guide.

-NAMes

writes the output file as a list file (formerly called a file of sequence names) suitable for input to other Wisconsin Package programs that support indirect file specification (see Chapter 2, Using Sequences of the User's Guide) . All of the output showing the location of the patterns found is suppressed when the output is written as a list file.

-SINce=6.90

limits the search to sequences that have been entered into the database or modified since June 1990. As this is being written, only the EMBL, GenBank, and SWISS-PROT databases support this feature.

-CIRcular

searches past the end of the sequence into the beginning of the sequence as if the molecule were continuous. Patterns that span the origin can only be found if the search is -CIRcular.

-ONEstrand

searches only the top strand of nucleotide sequences.

-SHOw

Normally, RFindPatterns shows that a file was searched only if there were one or more finds in sequence. With the -SHOw command-line option, RFindPatterns shows every file searched whether or not a pattern was actually found in it. (-SHOw is equivalent to setting -MINCuts= 0.)

-TERminal

writes output on the terminal screen and suppresses the output file query. If you use RFindPatterns often in this mode, you should assign a logical symbol that runs RFindPatterns with terminal output as the default. Answering the output file query with Term has the same effect on FindPatterns as this command-line option.

-BATch

submits the program to the batch queue for processing after prompting you for all required user inputs. Any information that would normally appear on the screen while the program is running is written into a log file. Whether that log file is deleted, printed, or saved to your current directory depends on how your system manager has set up the command that submits this program to the batch queue. All output files are written to your current directory, unless you direct the output to another directory when you specify the output file.

-MONitor

This program normally monitors its progress on your screen. However, when you use the -Default option to suppress all program interaction, you also suppress the monitor. You can turn it back on with this option. If your program is running in batch, the monitor will appear in the log file. If the monitor is slowing the program down, suppress it with -NOMONitor.

The descriptions of the exclusionary options below were written for the Wisconsin Package mapping programs. A find in these applications is referred to as a cut while a pattern is referred to as a restriction enzyme recognition site.

The options -SIXbase, -ONCe, -MINCuts, -MAXCuts, and -EXCLude all suppress the display of undesired enzymes. The list of excluded enzymes in the program output includes both enzymes that cut within excluded ranges and enzymes that do not cut the right number of times.

-SIXbase

searches only for enzymes with six or more bases in the recognition site. You can display the cuts from any enzyme in the enzyme data file that you take the trouble to name individually, but when you use * (meaning all), the program uses all of the other enzymes whose recognition sites have six or more non-N, non-X bases.

-ONCe

excludes, from the set you have chosen, those enzymes that cut your sequence more than once.

-MINCuts=2

excludes enzymes that do not cut at least two times.

-MAXCuts=2

excludes enzymes that cut more than two times.

-EXCLude=n1,n2[n3,n4,...]

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 not an even number of integers next to the qualifier.

-MISmatch=1

causes the program to recognize sites that are like the recognition site but with one (or more) mismatches. If you allow too many mismatches, you may get ridiculous results. The output from most mapping programs distinguishes between real sites and sites with one or more mismatches.

-PERFect

sets the program to look for a perfect alphabetic match between the site and the sequence. Ambiguity codes are normally expanded so that the site RXY would find sequences like ACT or GAC. With this switch the ambiguity codes are not expanded so the site RXY would only match the sequence RXY. This switch is not the same as -MISismatch=0.

-ALL

makes an overlap set map instead of the usual subset map. If your sequence is very ambiguous (as for instance a back-translated sequence would be) and you want to see where restriction sites could be, then you should create an overlap-set map. Overlap- set and subset pattern recognition are discussed in more detail in the Program Manual entry for the Window program.