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Split nucleotide sequence at restriction site

* Fragments* = restrict(

`SeqNT`

`Enzyme`

`Fragments`

`SeqNT`

`NTPattern`

`Position`

[

`Fragments`

`CuttingSites`

[

`Fragments`

`CuttingSites`

`Lengths`

... = restrict(..., 'PartialDigest',

`PartialDigestValue`

`SeqNT` | One of the following: Character vector of codes specifying a nucleotide sequence. For valid letter codes, see the table Mapping Nucleotide Letter Codes to Integers. Row vector of integers specifying a nucleotide sequence. For valid integers, see the table Mapping Nucleotide Integers to Letter Codes. MATLAB ^{®}structure containing a`Sequence` field that contains a nucleotide sequence, such as returned by`fastaread` ,`fastqread` ,`emblread` ,`getembl` ,`genbankread` , or`getgenbank` .
| |

`Enzyme` | Character vector specifying a name of a restriction enzyme
from REBASE
| |

`NTPattern` | Short nucleotide sequence recognition pattern to search
for in can
be either of the following: `NTPattern` Character vector Regular expression (MATLAB)
| |

`Position` | Either of the following: Integer specifying a position in the to cut, relative to`SeqNT` .`NTPattern` Two-element vector specifying two positions in the to cut, relative to`SeqNT` .`NTPattern`
| |

`PartialDigestValue` | Value from |

cuts * Fragments* = restrict(

`SeqNT`

`Enzyme`

`SeqNT`

`Enzyme`

`restrict`

function stores
the return values in `Fragments`

cuts * Fragments* = restrict(

`SeqNT`

`NTPattern`

`Position`

`SeqNT`

`NTPattern`

`Position`

`[`

returns a numeric vector with the indices
representing the cutting sites. The * Fragments*,

`CuttingSites`

`restrict`

function
adds a `0`

to the beginning of the `CuttingSites`

`CuttingSites`

`Fragments`

`CuttingSites`

+ 1

to
point to the first base of every fragment respective to the original
sequence.`[`

returns a numeric vector with the lengths
of every fragment.* Fragments*,

`CuttingSites`

`Lengths`

simulates
a partial digest where each restriction site in the sequence has a

... = restrict(..., 'PartialDigest', * PartialDigestValue*)

`PartialDigestValue`

REBASE, the Restriction Enzyme Database, is a collection of information about restriction enzymes and related proteins. For more information about REBASE or to search REBASE for the name of a restriction enzyme, see:

**Splitting a Nucleotide Sequence by Specifying an Enzyme**

Enter a nucleotide sequence.

`Seq = 'AGAGGGGTACGCGCTCTGAAAAGCGGGAACCTCGTGGCGCTTTATTAA';`

Use the restriction enzyme

`HspAI`

(which specifies a recognition sequence of`GCGC`

and a cleavage position of`1`

) to cleave the nucleotide sequence.`fragmentsEnzyme = restrict(Seq,'HspAI')`

MATLAB returns:

fragmentsEnzyme = 'AGAGGGGTACG' 'CGCTCTGAAAAGCGGGAACCTCGTGG' 'CGCTTTATTAA'

**Splitting a Nucleotide Sequence by Specifying a Pattern and
Position**

Enter a nucleotide sequence.

`Seq = 'AGAGGGGTACGCGCTCTGAAAAGCGGGAACCTCGTGGCGCTTTATTAA';`

Use the sequence pattern

`GCGC`

with the point of cleavage at position`3`

to cleave the nucleotide sequence.`fragmentsPattern = restrict(Seq,'GCGC',3)`

MATLAB returns:

fragmentsPattern = 'AGAGGGGTACGCG' 'CTCTGAAAAGCGGGAACCTCGTGGCG' 'CTTTATTAA'

**Splitting a Nucleotide Sequence by Specifying a Regular Expression
for the Pattern**

Enter a nucleotide sequence.

`Seq = 'AGAGGGGTACGCGCTCTGAAAAGCGGGAACCTCGTGGCGCTTTATTAA';`

Use a regular expression to specify the sequence pattern.

`fragmentsRegExp = restrict(Seq,'GCG[^C]',3)`

MATLAB returns:

fragmentsRegExp = 'AGAGGGGTACGCGCTCTGAAAAGCG' 'GGAACCTCGTGGCGCTTTATTAA'

**Returning the Cutting Sites and Fragment Lengths**

Enter a nucleotide sequence.

`Seq = 'AGAGGGGTACGCGCTCTGAAAAGCGGGAACCTCGTGGCGCTTTATTAA';`

Capture the cutting sites and fragment lengths as well as the fragments.

`[fragments, cut_sites, lengths] = restrict(Seq,'HspAI')`

MATLAB returns:

fragments = 'AGAGGGGTACG' 'CGCTCTGAAAAGCGGGAACCTCGTGG' 'CGCTTTATTAA' cut_sites = 0 11 37 lengths = 11 26 11

**Splitting a Double-Stranded Nucleotide Sequence**

Some enzymes specify cutting rules for both a strand and its
complement strand. `restrict`

applies the cutting
rule only for the 5' —> 3' strand. You can apply this rule
manually for the complement strand.

Enter a nucleotide sequence.

seq = 'CCCGCNNNNNNN';

Use the

`seqcomplement`

function to determine the complement strand, which is in the 3' —> 5' direction.seqc = seqcomplement(seq)

MATLAB returns:

seqc = GGGCGNNNNNNN

Cut the first strand using the restriction enzyme

`FauI`

(which specifies a recognition sequence pattern of`CCCGC`

and a cleavage position of`9`

).cuts_strand1 = restrict(seq, 'FauI')

MATLAB returns:

cuts_strand1 = 'CCCGCNNNN' 'NNN'

Cut the complement strand according the rule specified by

`FauI`

(which specifies a recognition sequence pattern of`GGGCG`

with the point of cleavage at position`11`

).cuts_strand2 = restrict(seqc, 'GGGCG', 11)

MATLAB returns:

cuts_strand2 = 'GGGCGNNNNNN' 'N'

[1] Roberts, R.J., Vincze, T., Posfai, J.,
and Macelis, D. (2007). REBASE—enzymes and genes for DNA restriction
and modification. Nucl. Acids Res. *35*, D269–D270.

[2] Official REBASE Web site: `http://rebase.neb.com`

.

`cleave`

| `cleavelookup`

| `rebasecuts`

| `regexp`

| `seq2regexp`

| `seqcomplement`

| `seqshowwords`

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