Restriction Enzyme

Sample code :

/**
  * Here is some samples of how to use the functions
  * @param   RestrictionEnzymeInterface  $restrictionEnzymeManager
  * @param   SequenceInterface           $sequenceManager
  * @param   SequenceAlignmentInterface  $sequenceAlignmentManager
  * @return  Response
  * @throws  \Exception
  */
public function restrictionenzyme(
    RestrictionEnzymeInterface $restrictionEnzymeManager,
    SequenceInterface $sequenceManager,
    SequenceAlignmentInterface $sequenceAlignmentManager
) {
    $sequenceAlignmentManager->setFilename("data/fasta-2.txt");
    $sequenceAlignmentManager->setFormat("FASTA");
    $sequenceAlignmentManager->parseFile();
    $oSequence = $sequenceAlignmentManager->getSeqSet()->offsetGet(0);
    $oSequence->setMolType("DNA");
    $sequenceManager->setSequence($oSequence);
    $restrictionEnzymeManager->setSequenceManager($sequenceManager);
 
    // Gets the enzyme "AatI" properties
    $restrictionEnzymeManager->parseEnzyme('AatI', null, null, "inner");
    $oEnzymeParsed = $restrictionEnzymeManager->getEnzyme();
 
    // Cuts a DNA sequence into fragments using the restriction enzyme object - patpos group
    $sCutseq = $restrictionEnzymeManager->cutSeq();
    // Patposo group
    $sCutseq2 = $restrictionEnzymeManager->cutSeq('O');
 
    // Searching the database (api) of endonucleases for a particular restriction enzyme
    $aList = $restrictionEnzymeManager->findRestEn("AGGCCT"); // fetch pattern only
    $aList2 = $restrictionEnzymeManager->findRestEn("AGGCCT",3); // fetch pattern and cutpos
    $aList3 = $restrictionEnzymeManager->findRestEn(null,3); // fetch Cutpos
    $aList4 = $restrictionEnzymeManager->findRestEn(null,null, 6); // fetch Length
    $aList5 = $restrictionEnzymeManager->findRestEn(null,3, 6); // fetch Cutpos And Plen
 
    return $this->render('default/restrictionenzyme.html.twig',
        [
            "enzymeParsed"  => $oEnzymeParsed,
            "cutseq"        => $sCutseq,
            "cutseq2"       => $sCutseq2,
            "list"          => $aList,
            "list2"         => $aList2,
            "list3"         => $aList3,
            "list4"         => $aList4,
            "list5"         => $aList5
        ]
    );
}

Result :

Gets the enzyme "AatI" properties

Cuts a DNA sequence into fragments using the restriction enzyme object (patpos group)

0 : "GGCAGATTCCCCCTAGACCCGCCCGCACCATGGTCAGGCATGCCCCTCCTCATCGCTGGGCACAGCCCAGAGGGTATAAACAGTGCTGGAGGCTGGCGGGGCAGGCCAGCTGAGTCCTGAGCAGCAGCCCAGCGCAGCCACCGAGACACCATGAGAGCCCTCACACTCCTCGCCCTATTGGCCCTGGCCGCACTTTGCATCGCTGGCCAGGCAGGTGAGTGCCCCCACCTCCCCTCAGGCCGCATTGCAGTGGGGGCTGAGAGGAGGAAGCACCATGGCCCACCTCTTCTCACCCCTTTGGCTGGCAGTCCCTTTGCAGTCTAACCACCTTGTTGCAGGCTCAATCCATTTGCCCCAGCTCTGCCCTTGCAGAGGGAGAGGAGGGAAGAGCAAGCTGCCCGAGACGCAGGGGAAGGAGGATGAGGGCCCTGGGGATGAGCTGGGGTGAACCAGGCTCCCTTTCCTTTGCAGGTGCGAAGCCCAGCGGTGCAGAGTCCAGCAAAGGTGCAGGTATGAGGATGGACCTGATGGGTTCCTGGACCCTCCCCTCTCACCCTGGTCCCTCAGTCTCATTCCCCCACTCCTGCCACCTCCTGTCTGGCCATCAGGAAGGCCAGCCTGCTCCCCACCTGATCCTCCCAAACCCAGAGCCACCTGATGCCTGCCCCTCTGCTCCACAGCCTTTGTGTCCAAGCAGGAGGGCAGCGAGGTAGTGAAGAGACCCAGGCGCTACCTGTATCAATGGCTGGGGTGAGAGAAAAGGCAGAGCTGGGCCAAGGCCCTGCCTCTCCGGGATGGTCTGTGGGGGAGCTGCAGCAGGGAGTGGCCTCTCTGGGTTGTGGTGGGGGTACAGGCAGCCTGCCCTGGTGGGCACCCTGGAGCCCCATGTGTAGGGAGAGGAGGGATGGGCATTTTGCACGGGGGCTGATGCCACCACGTCGGGTGTCTCAGAGCCCCAGTCCCCTACCCGGATCCCCTGGAGCCCAGGAGGGAGGTGTGTGAGCTCAATCCGGACTGTGACGAGTTGGCTGACCACATCGGCTTTCAGGAGG"
1 : "CCTATCGGCGCTTCTACGGCCCGGTCTAGGGTGTCGCTCTGCTGGCCTGGCCGGCAACCCCAGTTCTGCTCCTCTCCAGGCACCCTTCTTTCCTCTTCCCCTTGCCCTTGCCCTGACCTCCCAGCCCTATGGATGTGGGGTCCCCATCATCCCAGCTGCTCCCAAATAAACTCCAGAAG"

Cuts a DNA sequence into fragments using the restriction enzyme object (patposo group)

0 : "GGCAGATTCCCCCTAGACCCGCCCGCACCATGGTCAGGCATGCCCCTCCTCATCGCTGGGCACAGCCCAGAGGGTATAAACAGTGCTGGAGGCTGGCGGGGCAGGCCAGCTGAGTCCTGAGCAGCAGCCCAGCGCAGCCACCGAGACACCATGAGAGCCCTCACACTCCTCGCCCTATTGGCCCTGGCCGCACTTTGCATCGCTGGCCAGGCAGGTGAGTGCCCCCACCTCCCCTCAGGCCGCATTGCAGTGGGGGCTGAGAGGAGGAAGCACCATGGCCCACCTCTTCTCACCCCTTTGGCTGGCAGTCCCTTTGCAGTCTAACCACCTTGTTGCAGGCTCAATCCATTTGCCCCAGCTCTGCCCTTGCAGAGGGAGAGGAGGGAAGAGCAAGCTGCCCGAGACGCAGGGGAAGGAGGATGAGGGCCCTGGGGATGAGCTGGGGTGAACCAGGCTCCCTTTCCTTTGCAGGTGCGAAGCCCAGCGGTGCAGAGTCCAGCAAAGGTGCAGGTATGAGGATGGACCTGATGGGTTCCTGGACCCTCCCCTCTCACCCTGGTCCCTCAGTCTCATTCCCCCACTCCTGCCACCTCCTGTCTGGCCATCAGGAAGGCCAGCCTGCTCCCCACCTGATCCTCCCAAACCCAGAGCCACCTGATGCCTGCCCCTCTGCTCCACAGCCTTTGTGTCCAAGCAGGAGGGCAGCGAGGTAGTGAAGAGACCCAGGCGCTACCTGTATCAATGGCTGGGGTGAGAGAAAAGGCAGAGCTGGGCCAAGGCCCTGCCTCTCCGGGATGGTCTGTGGGGGAGCTGCAGCAGGGAGTGGCCTCTCTGGGTTGTGGTGGGGGTACAGGCAGCCTGCCCTGGTGGGCACCCTGGAGCCCCATGTGTAGGGAGAGGAGGGATGGGCATTTTGCACGGGGGCTGATGCCACCACGTCGGGTGTCTCAGAGCCCCAGTCCCCTACCCGGATCCCCTGGAGCCCAGGAGGGAGGTGTGTGAGCTCAATCCGGACTGTGACGAGTTGGCTGACCACATCGGCTTTCAGGAGG"
1 : "CCTATCGGCGCTTCTACGGCCCGGTCTAGGGTGTCGCTCTGCTGGCCTGGCCGGCAACCCCAGTTCTGCTCCTCTCCAGGCACCCTTCTTTCCTCTTCCCCTTGCCCTTGCCCTGACCTCCCAGCCCTATGGATGTGGGGTCCCCATCATCCCAGCTGCTCCCAAATAAACTCCAGAAG"

Searching our database of endonucleases for a particular restriction enzyme
Fetch pattern "AGGCCT" only

0 : "AatI"

Fetch pattern "AGGCCT" & cutpos 3

0 : "AatI"

Fetch cutpos 3 only

0 : "AatI"
1 : "Acc16I"
2 : "AccBSI"
3 : "AcvI"
4 : "AfeI"
5 : "AgSI"
6 : "AjiI"
7 : "AspLEI"
8 : "AssI"
9 : "BalI"
10 : "BmiI"
11 : "BsaAI"
12 : "Bsp68I"
13 : "BssNAI"
14 : "Bst4CI"
15 : "BstC8I"
16 : "BstKTI"
17 : "BstSNI"
18 : "DraI"
19 : "Ecl136II"
20 : "Eco32I"
21 : "EgeI"
22 : "HincII"
23 : "HpaI"
24 : "Hpy166II"
25 : "Hpy188I"
26 : "MspA1I"
27 : "NaeI"
28 : "PsiI"
29 : "PvuII"
30 : "SmaI"
31 : "SspI"
32 : "ZraI"

Fetch length 6 only

0 : "AatI"
1 : "AatII"
2 : "Acc16I"
3 : "Acc65I"
4 : "AccB1I"
5 : "AccBSI"
6 : "AccI"
7 : "AccIII"
8 : "AclI"
9 : "AcoI"
10 : "AcsI"
11 : "AcvI"
12 : "AcyI"
13 : "AfeI"
14 : "AflII"
15 : "AflIII"
16 : "AgeI"
17 : "AhlI"
18 : "AjiI"
19 : "Alw21I"
20 : "Alw44I"
21 : "Ama87I"
22 : "ApaI"
23 : "AseI"
24 : "AspA2I"
25 : "AssI"
26 : "AsuII"
27 : "AsuNHI"
28 : "BaeGI"
29 : "BalI"
30 : "BamHI"
31 : "BanII"
32 : "BanIII"
33 : "BauI"
34 : "BbeI"
35 : "BbuI"
36 : "BclI"
37 : "BfmI"
38 : "BfoI"
39 : "BglII"
40 : "BmiI"
41 : "BmtI"
42 : "BpvUI"
43 : "BsaAI"
44 : "BsaJI"
45 : "BsaWI"
46 : "Bse118I"
47 : "BsePI"
48 : "BseX3I"
49 : "BseYI"
50 : "Bsh1285I"
51 : "BsiWI"
52 : "Bsp120I"
53 : "Bsp1286I"
54 : "Bsp1407I"
55 : "Bsp19I"
56 : "Bsp68I"
57 : "BspHI"
58 : "BspLU11I"
59 : "BspMAI"
60 : "BssNAI"
61 : "BssT1I"
62 : "BstC8I"
63 : "BstDSI"
64 : "BstNSI"
65 : "BstSNI"
66 : "BstX2I"
67 : "Cfr42I"
68 : "Cfr9I"
69 : "CfrI"
70 : "DinI"
71 : "DraI"
72 : "Ecl136II"
73 : "Eco32I"
74 : "EcoRI"
75 : "EcoT22I"
76 : "EgeI"
77 : "FauNDI"
78 : "GsaI"
79 : "HincII"
80 : "HindIII"
81 : "HpaI"
82 : "Hpy166II"
83 : "Hpy188III"
84 : "KasI"
85 : "KpnI"
86 : "KroI"
87 : "MfeI"
88 : "MluI"
89 : "MspA1I"
90 : "NaeI"
91 : "PaeR7I"
92 : "PsiI"
93 : "Psp124BI"
94 : "PvuII"
95 : "SalI"
96 : "SmaI"
97 : "SmlI"
98 : "SspI"
99 : "TatI"
100 : "XbaI"
101 : "ZraI"

Fetch length 6 and cutpos 3 (no results)