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vectorstrip

vectorstrip is useful for stripping vector sequence from the ends of sequences of interest.

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 lowercase, and the vector sequence is represented in uppercase. This makes it easy to see the sequence trimming.

  1. Running vectorstrip on a list of sequences with default parameters:

    % 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
   
% 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 percent mismatch, then asking only for best hits:

    % 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 percent mismatch, then asking for all hits:

    % 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:

    % 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

Mandatory qualifiers (bold if not always prompted):

[-sequence] (seqall)

Sequence database USA.

[-[no]vectorfile] (boolean)

Are your vector sequences in a file?

* [-vectors] (infile)

Name of vectorfile.

-mismatch (integer)

Max allowed percentage mismatch.

-[no]besthits (boolean)

Show only the best hits (minimize mismatches)?

-linkera (string)

5' sequence.

-linkerb (string)

3' sequence.

[-outf] (outfile)

Output filename.

[-outseq] (seqoutall)

Output sequence(s) USA .
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