
                            EMBOSS: vectorstrip
     _________________________________________________________________
   
                              Program vectorstrip
                                       
Function

   Strips out DNA between a pair of vector sequences
   
Description

   vectorstrip is intended to be useful for stripping vector sequence
   from the ends of sequences of interest. For example, if a fragment has
   been cloned into a vector and then sequenced, the sequence may contain
   vector data eg from the cloning polylinker at the 5' and 3' ends of
   the sequence. vectorstrip will remove these contaminating regions and
   output trimmed sequence ready for input into another application.
   
   vectorstrip is suitable for use with low quality sequence data as it
   can allow for mismatches between the sequence and the vector patterns
   provided. You can specify the maximum level of mismatch expected.
   
   Vector data can either be provided in a file or interactively. If
   presented in a file, vectorstrip will search all input sequences with
   all vectors listed in that file. The intention is that the user can
   maintain a single file for use with vectorstrip, containing all the
   linker sequences commonly used in the laboratory.
   
   The two patterns for each vector are searched separately against the
   sequence. Once the search is completed, each of the hits of the 5'
   sequence is paired with each of the hits of the 3' sequence and the
   resulting subsequences are output. For example, if the 5' sequence
   matches the sequence from (a) position 30-60, and(b)position 70-100,
   and the 3' sequence matches from 150-175, then two subsequences will
   be output: from 61-149, and from 101-149. The lower the quality of the
   sequence, the more likely multiple hits become if nonzero mismatches
   are accepted.
   
   Default behaviour is to report only the best matches between the
   vector patterns and the sequence. This means that if you specify a
   maximum mismatch level of 10%, but the vector patterns match the
   sequence with zero mismatches, the search will stop and the program
   will output only these "best" matches. If there are no perfect
   matches, the program will try searching again allowing 1 mismatch,
   then 2, and so on until either the patterns match the sequence or the
   maximum specified mismatch level is exceeded. You can tell vectorstrip
   to show all possible matches up to your specified maximum level, as
   illustrated in the examples below.
   
Usage

   Here are several examples of running vectorstrip. The vectorfile and
   the sequence files used in these example are given below. In each
   case, the same fragment has been cloned into the XhoI site of the
   polylinker of each vector. The cloned fragment is represented in lower
   case and the vector sequence in upper case so the sequence trimming
   can be readily seen.
    1. Running vectorstrip on a list of sequences with default parameters
unix % vectorstrip @seqs.list
Strips out DNA between a pair of vector sequences
Are your vector sequences in a file? [Y]:
Name of vectorfile: vectors
Max allowed % mismatch [10]:
Show only the best hits (minimise mismatches)? [Y]:
Output file [pbluescript.vectorstrip]:stdout
Output sequence [pbluescript.fasta]:

Sequence: pBlueScript    Vector: pTYB1  No match


Sequence: pBlueScript    Vector: pBS_KS+
5' sequence matches:
        From 67 to 83 with 0 mismatches
3' sequence matches:
        From 205 to 219 with 0 mismatches
Sequences output to file:
        from 84 to 204
                tcgagagccgtattgcgatatagcgcacatgcgttggacacagatgagca
                cacagtgacatgagagacacagatatagagacagatagacgatagacaga
                cagcatatatagacagatagc
        sequence trimmed from 5' end:
                GGAAACAGCTAATGACCATGATTACGCCAAGCGCGCAATTAACCCTCACT
                AAAGGGAACAAAAGCTGGGTACCGGGCCCCCCC
        sequence trimmed from 3' end:
                TCGAGGTCGACGGTATCGATAAGCTTGATATCG


Sequence: pBlueScript    Vector: pLITMUS        No match

Sequence: litmus.seq     Vector: pTYB1  No match

Sequence: litmus.seq     Vector: pBS_KS+        No match


Sequence: litmus.seq     Vector: pLITMUS
5' sequence matches:
        From 43 to 61 with 0 mismatches
3' sequence matches:
        From 183 to 199 with 0 mismatches
Sequences output to file:
        from 62 to 182
                tcgagagccgtattgcgatatagcgcacatgcgttggacacagatgagca
                cacagtgacatgagagacacagatatagagacagatagacgatagacaga
                cagcatatatagacagatagc
        sequence trimmed from 5' end:
                TCTAGAACCGGTGACGTCTCCCATGGTGAAGCTTGGATCCACGATATCCT
                GCAGGAATTCC


Sequence: pTYB1.seq      Vector: pTYB1
5' sequence matches:
        From 40 to 58 with 0 mismatches
3' sequence matches:
        From 180 to 196 with 0 mismatches
Sequences output to file:
        from 59 to 179
                tcgagagccgtattgcgatatagcgcacatgcgttggacacagatgagca
                cacagtgacatgagagacacagatatagagacagatagacgatagacaga
                cagcatatatagacagatagc
        sequence trimmed from 5' end:
                CTTTAAGAAGGAGATATACATATGGCTAGCTCGCGAGTCGACGGCGGCCG
                CGAATTCC
        sequence trimmed from 3' end:
                TCGAGGGCTCTTCCTGCTTTGCCAAGGGTACCAATGTTTTAATGGCGGAT


Sequence: pTYB1.seq      Vector: pBS_KS+        No match

Sequence: pTYB1.seq      Vector: pLITMUS        No match


unix % more pbluescript.fasta
>pBlueScript_from_84_to_204 KS+
tcgagagccgtattgcgatatagcgcacatgcgttggacacagatgagcacacagtgaca
tgagagacacagatatagagacagatagacgatagacagacagcatatatagacagatag
c
>litmus.seq_from_62_to_182
tcgagagccgtattgcgatatagcgcacatgcgttggacacagatgagcacacagtgaca
tgagagacacagatatagagacagatagacgatagacagacagcatatatagacagatag
c
>pTYB1.seq_from_59_to_179
tcgagagccgtattgcgatatagcgcacatgcgttggacacagatgagcacacagtgaca
tgagagacacagatatagagacagatagacgatagacagacagcatatatagacagatag
c
    2. Running vectorstrip allowing maximum 30% mismatch, and asking only
       for best hits
unix % vectorstrip litmus.seq
Strips out DNA between a pair of vector sequences
Are your vector sequences in a file? [Y]:
Name of vectorfile: vectors
Max allowed % mismatch [10]: 30
Show only the best hits (minimise mismatches)? [Y]:
Output file [litmus.vectorstrip]: stdout
Output sequence [litmus.fasta]:

Sequence: litmus.seq     Vector: pTYB1  No match

Sequence: litmus.seq     Vector: pBS_KS+        No match


Sequence: litmus.seq     Vector: pLITMUS
5' sequence matches:
        From 43 to 61 with 0 mismatches
3' sequence matches:
        From 183 to 199 with 0 mismatches
Sequences output to file:
        from 62 to 182
                tcgagagccgtattgcgatatagcgcacatgcgttggacacagatgagca
                cacagtgacatgagagacacagatatagagacagatagacgatagacaga
                cagcatatatagacagatagc
        sequence trimmed from 5' end:
                TCTAGAACCGGTGACGTCTCCCATGGTGAAGCTTGGATCCACGATATCCT
                GCAGGAATTCC
        sequence trimmed from 3' end:
                TCGAGACCGTACGTGCGCGCGAATGCATCCAGATCTTCCCTCTAGTCAAG
                GCCTTAAGTGAGTCGTATTACGGA
    3. Running vectorstrip allowing maximum 30% mismatch, and asking for
       all hits
unix % vectorstrip litmus.seq
Strips out DNA between a pair of vector sequences
Are your vector sequences in a file? [Y]:
Name of vectorfile: vectors
Max allowed % mismatch [10]: 30
Show only the best hits (minimise mismatches)? [Y]: N
Output file [litmus.vectorstrip]: stdout
Output sequence [litmus.fasta]:

Sequence: litmus.seq     Vector: pTYB1  No match

Sequence: litmus.seq     Vector: pBS_KS+        No match


Sequence: litmus.seq     Vector: pLITMUS
5' sequence matches:
        From 43 to 61 with 0 mismatches
3' sequence matches:
        From 183 to 199 with 0 mismatches
        From 228 to 244 with 5 mismatches
Sequences output to file:
        from 62 to 182
                tcgagagccgtattgcgatatagcgcacatgcgttggacacagatgagca
                cacagtgacatgagagacacagatatagagacagatagacgatagacaga
                cagcatatatagacagatagc
        sequence trimmed from 5' end:
                TCTAGAACCGGTGACGTCTCCCATGGTGAAGCTTGGATCCACGATATCCT
                GCAGGAATTCC
        sequence trimmed from 3' end:
                TCGAGACCGTACGTGCGCGCGAATGCATCCAGATCTTCCCTCTAGTCAAG
                GCCTTAAGTGAGTCGTATTACGGA

        from 62 to 227
                tcgagagccgtattgcgatatagcgcacatgcgttggacacagatgagca
                cacagtgacatgagagacacagatatagagacagatagacgatagacaga
                cagcatatatagacagatagcTCGAGACCGTACGTGCGCGCGAATGCATC
                CAGATCTTCCCTCTAG
        sequence trimmed from 5' end:
                TCTAGAACCGGTGACGTCTCCCATGGTGAAGCTTGGATCCACGATATCCT
                GCAGGAATTCC
        sequence trimmed from 3' end:
                TCAAGGCCTTAAGTGAGTCGTATTACGGA
    4. Running vectorstrip against a sequence containing Ns
unix % vectorstrip pTYB1_N.seq
Strips out DNA between a pair of vector sequences
Are your vector sequences in a file? [Y]:
Name of vectorfile: vectors
Max allowed % mismatch [10]: 30
Show only the best hits (minimise mismatches)? [Y]:
Output file [ptyb1.vectorstrip]: stdout
Output sequence [ptyb1.fasta]:


Sequence: pTYB1.seq      Vector: pTYB1
5' sequence matches:
        From 40 to 58 with 2 mismatches
3' sequence matches:
        From 180 to 196 with 2 mismatches
Sequences output to file:
        from 59 to 179
                tcnagagccgtatngcgatatngcgcacatgcgntggacacagangagca
                cacagtnacatgagagncacagatntagagacagatngacgataganaga
                cagcatanatagacanatagc
        sequence trimmed from 5' end:
                CTTTAAGNAGGAGANATACANATGGCNAGCTCGCGANTCGACGGCGGNCG
                CGAATNCC
        sequence trimmed from 3' end:
                TCGNGGGCTCTTCCNGCTTTGCCANGGGTACCAANGTTTTAATGGCNGAT


Sequence: pTYB1.seq      Vector: pBS_KS+        No match

Sequence: pTYB1.seq      Vector: pLITMUS        No match

Command line arguments

   Mandatory qualifiers (* if not always prompted):
  [-sequence]          seqall     Sequence database USA
  [-[no]vectorfile]    bool       Are your vector sequences in a file?
* [-vectors]           infile     Name of vectorfile
   -mismatch           integer    Max allowed % mismatch
   -[no]besthits       bool       Show only the best hits (minimise
                                  mismatches)?
*  -linkera            string     5' sequence
*  -linkerb            string     3' sequence
  [-outf]              outfile    Output file name
  [-outseq]            seqoutall  Output sequence(s) USA

   Optional qualifiers: (none)
   Advanced qualifiers: (none)
   General qualifiers:
  -help                bool       report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   

   Mandatory qualifiers Allowed values Default
   [-sequence]
   (Parameter 1) Sequence database USA Readable sequence(s) Required
   [-[no]vectorfile]
   (Parameter 2) Are your vector sequences in a file? Yes/No Yes
   [-vectors]
   (Parameter 3) Name of vectorfile Input file Required
   -mismatch Max allowed % mismatch Any integer value 10
   -[no]besthits Show only the best hits (minimise mismatches)? Yes/No
   Yes
   -linkera 5' sequence Any string is accepted An empty string is
   accepted
   -linkerb 3' sequence Any string is accepted An empty string is
   accepted
   [-outf]
   (Parameter 4) Output file name Output file <sequence>.vectorstrip
   [-outseq]
   (Parameter 5) Output sequence(s) USA Writeable sequence(s)
   <sequence>.format
   Optional qualifiers Allowed values Default
   (none)
   Advanced qualifiers Allowed values Default
   (none)
   
Input file format

   Each line should contain the name of the vector, the 5' pattern and
   the 3' pattern.
   Lines beginning with # are treated as comments and ignored.
   If only one vector sequence is given in the it will be assumed that
   this is the 5' pattern.
   If a vector name is given but no pattern data, the vector will not be
   used.
   
   For example, the file used in the examples above is:
pTYB1   GACGGCGGCCGCGAATTCC     TCGAGGGCTCTTCCTGC
pBS_KS+ GGGTACCGGGCCCCCCC       TCGAGGTCGACGGTA
pLITMUS GATATCCTGCAGGAATTCC     TCGAGACCGTACGTGCG

   The sequence files used in the examples above are:
    1. seqs.list
bluescript.seq
litmus.seq
pTYB1.seq
    2. bluescript.seq
> pBlueScript KS+
GGAAACAGCTAATGACCATGATTACGCCAAGCGCGCAATTAACCCTCACTAAAGGGAAC
AAAAGCTGGGTACCGGGCCCCCCCtcgagagccgtattgcgatatagcgcacatgcgtt
ggacacagatgagcacacagtgacatgagagacacagatatagagacagatagacgata
gacagacagcatatatagacagatagcTCGAGGTCGACGGTATCGATAAGCTTGATATCG
    3. litmus.seq
> litmus.seq
TCTAGAACCGGTGACGTCTCCCATGGTGAAGCTTGGATCCACGATATCCTGCAGGAATT
CCtcgagagccgtattgcgatatagcgcacatgcgttggacacagatgagcacacagtg
acatgagagacacagatatagagacagatagacgatagacagacagcatatatagacag
atagcTCGAGACCGTACGTGCGCGCGAATGCATCCAGATCTTCCCTCTAGTCAAGGCCT
TAAGTGAGTCGTATTACGGA
    4. pTYB1.seq
>pTYB1.seq
CTTTAAGAAGGAGATATACATATGGCTAGCTCGCGAGTCGACGGCGGCCGCGAATTCCtc
gagagccgtattgcgatatagcgcacatgcgttggacacagatgagcacacagtgacatg
agagacacagatatagagacagatagacgatagacagacagcatatatagacagatagcT
CGAGGGCTCTTCCTGCTTTGCCAAGGGTACCAATGTTTTAATGGCGGAT
    5. pTYB1_N.seq
>pTYB1.seq lower quality
CTTTAAGNAGGAGANATACANATGGCNAGCTCGCGANTCGACGGCGGNCGCGAATNCCtc
nagagccgtatngcgatatngcgcacatgcgntggacacagangagcacacagtnacatg
agagncacagatntagagacagatngacgataganagacagcatanatagacanatagcT
CGNGGGCTCTTCCNGCTTTGCCANGGGTACCAANGTTTTAATGGCNGAT

   In each case the vector sequence is given in upper case and the cloned
   sequence in lower case.
   
Output file format

   Two types of output file are produced:
    1. The sequence file(s) - contain the trimmed subsequence(s) produced
       by vectorstrip either all in one file, or in separate files if the
       command line flag -ossingle is used.
    2. Results summary file eg
Sequence: pTYB1.seq      Vector: pTYB1
5' sequence matches:
        From 40 to 58 with 2 mismatches
3' sequence matches:
        From 180 to 196 with 2 mismatches
Sequences output to file:
        from 59 to 179
                tcnagagccgtatngcgatatngcgcacatgcgntggacacagangagca
                cacagtnacatgagagncacagatntagagacagatngacgataganaga
                cagcatanatagacanatagc
        sequence trimmed from 5' end:
                CTTTAAGNAGGAGANATACANATGGCNAGCTCGCGANTCGACGGCGGNCG
                CGAATNCC
        sequence trimmed from 3' end:
                TCGNGGGCTCTTCCNGCTTTGCCANGGGTACCAANGTTTTAATGGCNGAT

Data files

   None.
   
Notes

   None.
   
References

   None.
   
Warnings

   None.
   
Diagnostic Error Messages

    1.
No suitable vectors found - exiting
       indicates that the 5' and 3' patterns for the vectors were blank -
       usually this is as a result of an empty vectorfile.
    2.
Illegal pattern
       indicates that one of the vector patterns could not be compiled
       and therefore cannot be searched.
    3.
5' and 3' sequence matches are identical; inconclusive
       indicates that the 5' and 3' patterns provided were identical, and
       that they only match the sequence once. Thus the program cannot
       determine which part of the sequence is vector and which is
       insert.
       
Exit status

   It always exits with status 0.
   
Known bugs

   None.
   
See also

   Program name                          Description
   biosed       Replace or delete sequence sections
   cutseq       Removes a specified section from a sequence
   degapseq     Removes gap characters from sequences
   descseq      Alter the name or description of a sequence
   entret       Reads and writes (returns) flatfile entries
   extractfeat  Extract features from a sequence
   extractseq   Extract regions from a sequence
   listor       Writes a list file of the logical OR of two sets of sequences
   maskfeat     Mask off features of a sequence
   maskseq      Mask off regions of a sequence
   newseq       Type in a short new sequence
   noreturn     Removes carriage return from ASCII files
   notseq       Excludes a set of sequences and writes out the remaining ones
   nthseq       Writes one sequence from a multiple set of sequences
   pasteseq     Insert one sequence into another
   revseq       Reverse and complement a sequence
   seqret       Reads and writes (returns) sequences
   seqretsplit  Reads and writes (returns) sequences in individual files
   splitter     Split a sequence into (overlapping) smaller sequences
   swissparse   Retrieves sequences from swissprot using keyword search
   trimest      Trim poly-A tails off EST sequences
   trimseq      Trim ambiguous bits off the ends of sequences
   union        Reads sequence fragments and builds one sequence
   yank         Reads a sequence range, appends the full USA to a list file
   
Author(s)

   This application was written by Val Curwen (vcurwen@hgmp.mrc.ac.uk)
   
History

   16 August 2000 - Val Curwen - Written.
   
Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.
   
Comments
