Package Bio :: Package Restriction :: Module Restriction
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Module Restriction

source code

Notes about the diverses class of the restriction enzyme implementation.

    RestrictionType is the type of all restriction enzymes.
----------------------------------------------------------------------------
    AbstractCut implements some methods that are common to all enzymes.
----------------------------------------------------------------------------
    NoCut, OneCut,TwoCuts   represent the number of double strand cuts
                            produced by the enzyme.
                            they correspond to the 4th field of the rebase
                            record emboss_e.NNN.
            0->NoCut    : the enzyme is not characterised.
            2->OneCut   : the enzyme produce one double strand cut.
            4->TwoCuts  : two double strand cuts.
----------------------------------------------------------------------------
    Meth_Dep, Meth_Undep    represent the methylation susceptibility to
                            the enzyme.
                            Not implemented yet.
----------------------------------------------------------------------------
    Palindromic,            if the site is palindromic or not.
    NotPalindromic          allow some optimisations of the code.
                            No need to check the reverse strand
                            with palindromic sites.
----------------------------------------------------------------------------
    Unknown, Blunt,         represent the overhang.
    Ov5, Ov3                Unknown is here for symetry reasons and
                            correspond to enzymes that are not characterised
                            in rebase.
----------------------------------------------------------------------------
    Defined, Ambiguous,     represent the sequence of the overhang.
    NotDefined
                            NotDefined is for enzymes not characterised in
                            rebase.

                            Defined correspond to enzymes that display a
                            constant overhang whatever the sequence.
                            ex : EcoRI. G^AATTC -> overhang :AATT
                                        CTTAA^G

                            Ambiguous : the overhang varies with the
                            sequence restricted.
                            Typically enzymes which cut outside their
                            restriction site or (but not always)
                            inside an ambiguous site.
                            ex:
                            AcuI CTGAAG(22/20)  -> overhang : NN
                            AasI GACNNN^NNNGTC  -> overhang : NN
                                 CTGN^NNNNNCAG

        note : these 3 classes refers to the overhang not the site.
           So the enzyme ApoI (RAATTY) is defined even if its restriction
           site is ambiguous.

                ApoI R^AATTY -> overhang : AATT -> Defined
                     YTTAA^R
           Accordingly, blunt enzymes are always Defined even
           when they cut outside their restriction site.
----------------------------------------------------------------------------
    Not_available,          as found in rebase file emboss_r.NNN files.
    Commercially_available
                            allow the selection of the enzymes according to
                            their suppliers to reduce the quantity
                            of results.
                            Also will allow the implementation of buffer
                            compatibility tables. Not implemented yet.

                            the list of suppliers is extracted from
                            emboss_s.NNN
----------------------------------------------------------------------------
    

Classes [hide private]
  FormattedSeq
FormattedSeq(seq, [linear=True])-> new FormattedSeq.
  RestrictionType
RestrictionType.
  AbstractCut
Implement the methods that are common to all restriction enzymes.
  NoCut
Implement the methods specific to the enzymes that do not cut.
  OneCut
Implement the methods specific to the enzymes that cut the DNA only once
  TwoCuts
Implement the methods specific to the enzymes that cut the DNA twice
  Meth_Dep
Implement the information about methylation.
  Meth_Undep
Implement information about methylation sensitibility.
  Palindromic
Implement the methods specific to the enzymes which are palindromic
  NonPalindromic
Implement the methods specific to the enzymes which are not palindromic
  Unknown
Implement the methods specific to the enzymes for which the overhang is unknown.
  Blunt
Implement the methods specific to the enzymes for which the overhang is blunt.
  Ov5
Implement the methods specific to the enzymes for which the overhang is recessed in 3'.
  Ov3
Implement the methods specific to the enzymes for which the overhang is recessed in 5'.
  Defined
Implement the methods specific to the enzymes for which the overhang and the cut are not variable.
  Ambiguous
Implement the methods specific to the enzymes for which the overhang is variable.
  NotDefined
Implement the methods specific to the enzymes for which the overhang is not characterised.
  Commercially_available
Implement the methods specific to the enzymes which are commercially available.
  Not_available
Implement the methods specific to the enzymes which are not commercially available.
  RestrictionBatch
  Analysis
  AanI
  AarI
  AasI
  AatII
  AbaSI
  AbsI
  Acc16I
  Acc36I
  Acc65I
  AccB1I
  AccB7I
  AccBSI
  AccI
  AccII
  AccIII
  AceIII
  AciI
  AclI
  AclWI
  AcoI
  AcsI
  AcuI
  AcvI
  AcyI
  AdeI
  AfaI
  AfeI
  AfiI
  AflII
  AflIII
  AgeI
  AgsI
  AhaIII
  AhdI
  AhlI
  AjiI
  AjnI
  AjuI
  AleI
  AlfI
  AloI
  AluBI
  AluI
  Alw21I
  Alw26I
  Alw44I
  AlwFI
  AlwI
  AlwNI
  Ama87I
  Aor13HI
  Aor51HI
  AoxI
  ApaBI
  ApaI
  ApaLI
  ApeKI
  ApoI
  ApyPI
  AquII
  AquIII
  AquIV
  ArsI
  AscI
  AseI
  Asi256I
  AsiGI
  AsiSI
  Asp700I
  Asp718I
  AspA2I
  AspBHI
  AspLEI
  AspS9I
  AssI
  AsuC2I
  AsuHPI
  AsuI
  AsuII
  AsuNHI
  AvaI
  AvaII
  AvaIII
  AvrII
  AxyI
  BaeGI
  BaeI
  BalI
  BamHI
  BanI
  BanII
  BarI
  BasI
  BauI
  Bbr7I
  BbrPI
  BbsI
  Bbv12I
  BbvCI
  BbvI
  BbvII
  BccI
  Bce83I
  BceAI
  BcefI
  BcgI
  BciT130I
  BciVI
  BclI
  BcnI
  BcoDI
  BcuI
  BdaI
  BetI
  BfaI
  BfiI
  BfmI
  BfoI
  BfrI
  BfuAI
  BfuCI
  BfuI
  BglI
  BglII
  BinI
  BisI
  BlnI
  BlpI
  BlsI
  BmcAI
  Bme1390I
  Bme18I
  BmeDI
  BmeRI
  BmeT110I
  BmgBI
  BmgI
  BmgT120I
  BmiI
  BmrFI
  BmrI
  BmsI
  BmtI
  BmuI
  BoxI
  BpiI
  BplI
  BpmI
  Bpu10I
  Bpu1102I
  Bpu14I
  BpuEI
  BpuMI
  BpvUI
  Bsa29I
  BsaAI
  BsaBI
  BsaHI
  BsaI
  BsaJI
  BsaWI
  BsaXI
  BsbI
  Bsc4I
  BscAI
  BscGI
  Bse118I
  Bse1I
  Bse21I
  Bse3DI
  Bse8I
  BseAI
  BseBI
  BseCI
  BseDI
  BseGI
  BseJI
  BseLI
  BseMI
  BseMII
  BseNI
  BsePI
  BseRI
  BseSI
  BseX3I
  BseXI
  BseYI
  BsgI
  Bsh1236I
  Bsh1285I
  BshFI
  BshNI
  BshTI
  BshVI
  BsiEI
  BsiHKAI
  BsiHKCI
  BsiI
  BsiSI
  BsiWI
  BsiYI
  BslFI
  BslI
  BsmAI
  BsmBI
  BsmFI
  BsmI
  BsnI
  Bso31I
  BsoBI
  Bsp119I
  Bsp120I
  Bsp1286I
  Bsp13I
  Bsp1407I
  Bsp143I
  Bsp1720I
  Bsp19I
  Bsp24I
  Bsp68I
  BspACI
  BspCNI
  BspD6I
  BspDI
  BspEI
  BspFNI
  BspGI
  BspHI
  BspLI
  BspLU11I
  BspMI
  BspMII
  BspNCI
  BspOI
  BspPI
  BspQI
  BspT104I
  BspT107I
  BspTI
  BsrBI
  BsrDI
  BsrFI
  BsrGI
  BsrI
  BsrSI
  BssAI
  BssECI
  BssHII
  BssKI
  BssMI
  BssNAI
  BssNI
  BssSI
  BssT1I
  Bst1107I
  Bst2BI
  Bst2UI
  Bst4CI
  Bst6I
  BstACI
  BstAFI
  BstAPI
  BstAUI
  BstBAI
  BstBI
  BstC8I
  BstDEI
  BstDSI
  BstEII
  BstENI
  BstF5I
  BstFNI
  BstH2I
  BstHHI
  BstKTI
  BstMAI
  BstMBI
  BstMCI
  BstMWI
  BstNI
  BstNSI
  BstOI
  BstPAI
  BstPI
  BstSCI
  BstSFI
  BstSLI
  BstSNI
  BstUI
  BstV1I
  BstV2I
  BstX2I
  BstXI
  BstYI
  BstZ17I
  BstZI
  Bsu15I
  Bsu36I
  BsuI
  BsuRI
  BtgI
  BtgZI
  BthCI
  BtrI
  BtsCI
  BtsI
  BtsIMutI
  BtuMI
  BveI
  Cac8I
  CaiI
  CauII
  CchII
  CchIII
  CciI
  CciNI
  Cdi630V
  CdiI
  CdpI
  CfoI
  Cfr10I
  Cfr13I
  Cfr42I
  Cfr9I
  CfrI
  Cgl13032I
  Cgl13032II
  ChaI
  CjeFIII
  CjeFV
  CjeI
  CjeNII
  CjeNIII
  CjeP659IV
  CjePI
  CjuI
  CjuII
  ClaI
  CpoI
  CseI
  CsiI
  Csp6I
  CspAI
  CspCI
  CspI
  CstMI
  CviAII
  CviJI
  CviKI_1
  CviQI
  CviRI
  DdeI
  DinI
  DpnI
  DpnII
  DraI
  DraII
  DraIII
  DraRI
  DrdI
  DrdII
  DriI
  DsaI
  DseDI
  EaeI
  EagI
  Eam1104I
  Eam1105I
  EarI
  EciI
  Ecl136II
  EclXI
  Eco105I
  Eco130I
  Eco147I
  Eco24I
  Eco31I
  Eco32I
  Eco47I
  Eco47III
  Eco52I
  Eco53kI
  Eco57I
  Eco57MI
  Eco72I
  Eco81I
  Eco88I
  Eco91I
  EcoHI
  EcoICRI
  EcoNI
  EcoO109I
  EcoO65I
  EcoRI
  EcoRII
  EcoRV
  EcoT14I
  EcoT22I
  EcoT38I
  EgeI
  EheI
  ErhI
  EsaBC3I
  EsaSSI
  Esp3I
  EspI
  FaeI
  FaiI
  FalI
  FaqI
  FatI
  FauI
  FauNDI
  FbaI
  FblI
  FinI
  FmuI
  Fnu4HI
  FnuDII
  FokI
  FriOI
  FseI
  Fsp4HI
  FspAI
  FspBI
  FspEI
  FspI
  GauT27I
  GdiII
  GlaI
  GluI
  GsaI
  GsuI
  HaeI
  HaeII
  HaeIII
  HapII
  HauII
  HgaI
  HgiAI
  HgiCI
  HgiEII
  HgiJII
  HhaI
  Hin1I
  Hin1II
  Hin4I
  Hin4II
  Hin6I
  HinP1I
  HincII
  HindII
  HindIII
  HinfI
  HpaI
  HpaII
  HphI
  Hpy166II
  Hpy178III
  Hpy188I
  Hpy188III
  Hpy8I
  Hpy99I
  Hpy99XIII
  Hpy99XIV
  HpyAV
  HpyCH4III
  HpyCH4IV
  HpyCH4V
  HpyF10VI
  HpyF3I
  HpySE526I
  Hsp92I
  Hsp92II
  HspAI
  Jma19592I
  KasI
  KflI
  Kpn2I
  KpnI
  KroI
  Ksp22I
  Ksp632I
  KspAI
  KspI
  Kzo9I
  LguI
  LpnI
  LpnPI
  Lsp1109I
  LweI
  MabI
  MaeI
  MaeII
  MaeIII
  MalI
  MaqI
  MauBI
  MbiI
  MboI
  MboII
  McaTI
  McrI
  MfeI
  MflI
  MhlI
  MjaIV
  MkaDII
  MlsI
  MluCI
  MluI
  MluNI
  Mly113I
  MlyI
  MmeI
  MnlI
  Mph1103I
  MreI
  MroI
  MroNI
  MroXI
  MscI
  MseI
  MslI
  Msp20I
  MspA1I
  MspCI
  MspI
  MspJI
  MspR9I
  MssI
  MstI
  MunI
  Mva1269I
  MvaI
  MvnI
  MvrI
  MwoI
  NaeI
  NarI
  NciI
  NcoI
  NdeI
  NdeII
  NgoAVIII
  NgoMIV
  NhaXI
  NheI
  NlaCI
  NlaIII
  NlaIV
  Nli3877I
  NmeAIII
  NmeDI
  NmuCI
  NotI
  NruI
  NsbI
  NsiI
  NspBII
  NspI
  NspV
  OliI
  PabI
  PacI
  PaeI
  PaeR7I
  PagI
  PalAI
  PasI
  PauI
  PceI
  PciI
  PciSI
  PcsI
  PctI
  PdiI
  PdmI
  PenI
  PfeI
  Pfl1108I
  Pfl23II
  PflFI
  PflMI
  PfoI
  PinAI
  PlaDI
  Ple19I
  PleI
  PluTI
  PmaCI
  PmeI
  PmlI
  PpiI
  PpsI
  Ppu10I
  Ppu21I
  PpuMI
  PscI
  PshAI
  PshBI
  PsiI
  Psp03I
  Psp124BI
  Psp1406I
  Psp5II
  Psp6I
  PspCI
  PspEI
  PspGI
  PspLI
  PspN4I
  PspOMI
  PspOMII
  PspPI
  PspPPI
  PspPRI
  PspXI
  PsrI
  PssI
  PstI
  PstNI
  PsuI
  PsyI
  PteI
  PvuI
  PvuII
  R2_BceSIV
  RceI
  RdeGBI
  RdeGBII
  RdeGBIII
  RflFIII
  RgaI
  RigI
  RlaI
  RleAI
  RpaB5I
  RpaBI
  RpaI
  RpaTI
  RruI
  RsaI
  RsaNI
  RseI
  Rsr2I
  RsrII
  SacI
  SacII
  SalI
  SanDI
  SapI
  SaqAI
  SatI
  Sau3AI
  Sau96I
  SauI
  SbfI
  ScaI
  SchI
  SciI
  ScrFI
  SdaI
  SdeAI
  SdeOSI
  SduI
  SecI
  SelI
  SetI
  SexAI
  SfaAI
  SfaNI
  SfcI
  SfeI
  SfiI
  SfoI
  Sfr274I
  Sfr303I
  SfuI
  SgeI
  SgfI
  SgrAI
  SgrBI
  SgrDI
  SgrTI
  SgsI
  SimI
  SlaI
  SmaI
  SmiI
  SmiMI
  SmlI
  SmoI
  SnaBI
  SnaI
  Sno506I
  SpeI
  SphI
  SplI
  SpoDI
  SrfI
  Sse232I
  Sse8387I
  Sse8647I
  Sse9I
  SseBI
  SsiI
  SspD5I
  SspDI
  SspI
  SstE37I
  SstI
  Sth132I
  Sth302II
  StrI
  StsI
  StuI
  StyD4I
  StyI
  SwaI
  T
  TaaI
  TaiI
  TaqI
  TaqII
  TasI
  TatI
  TauI
  TfiI
  Tru1I
  Tru9I
  TscAI
  TseFI
  TseI
  TsoI
  Tsp45I
  Tsp4CI
  TspDTI
  TspEI
  TspGWI
  TspMI
  TspRI
  TssI
  TstI
  TsuI
  Tth111I
  Tth111II
  UbaF11I
  UbaF12I
  UbaF13I
  UbaF14I
  UbaF9I
  UbaPI
  UcoMSI
  UnbI
  Van91I
  Vha464I
  VneI
  VpaK11AI
  VpaK11BI
  VspI
  WviI
  XagI
  XapI
  XbaI
  XceI
  XcmI
  XhoI
  XhoII
  XmaI
  XmaIII
  XmaJI
  XmiI
  XmnI
  XspI
  YkrI
  ZraI
  ZrmI
  Zsp2I
  newenz
Functions [hide private]
 
_check_bases(seq_string)
Check characters in a string (PRIVATE).
source code
Variables [hide private]
  enzymedict = {'AanI': {'charac': (3, -3, None, None, 'TTATAA')...
  typedict = {'type130': (('Palindromic', 'TwoCuts', 'Ov5', 'Amb...
  suppliers_dict = {'B': ('Life Technologies', ['MluI', 'SacI', ...
  ftp_emb_e = 'ftp://ftp.neb.com/pub/rebase/emboss_e.###'
  Indent = 4
  Rebase_name = 'anonymous'
  ftp_Rebase = 'ftp://ftp.neb.com/'
  ConsoleWidth = 80
  ftp_proxy = ''
  MaxSize = 6
  ftp_emb_s = 'ftp://ftp.neb.com/pub/rebase/emboss_s.###'
  NameWidth = 10
  Rebase_password = ''
  ftp_emb_r = 'ftp://ftp.neb.com/pub/rebase/emboss_r.###'
  matching = {'A': 'ARWMHVDN', 'B': 'CBDGHKMNSRTWVY', 'C': 'CYSM...
  CommOnly = RestrictionBatch(['AanI', 'AarI', 'AasI', 'AatII', ...
  NonComm = RestrictionBatch(['AceIII', 'AhaIII', 'AlwFI', 'AoxI...
  AllEnzymes = RestrictionBatch(['AanI', 'AarI', 'AasI', 'AatII'...
  __package__ = 'Bio.Restriction'
Function Details [hide private]

_check_bases(seq_string)

source code 
Check characters in a string (PRIVATE).

Remove digits and white space present in string. Allows any valid ambiguous
IUPAC DNA single letters codes (ABCDGHKMNRSTVWY, lower case are converted).

Other characters (e.g. symbols) trigger a TypeError.

Returns the string WITH A LEADING SPACE (!). This is for backwards
compatibility, and may in part be explained by the fact that
Bio.Restriction doesn't use zero based counting.


Variables Details [hide private]

enzymedict

Value:
{'AanI': {'charac': (3, -3, None, None, 'TTATAA'),
          'compsite': '(?P<AanI>TTATAA)',
          'dna': None,
          'freq': 4096,
          'fst3': -3,
          'fst5': 3,
          'inact_temp': 65,
          'opt_temp': 37,
...

typedict

Value:
{'type130': (('Palindromic',
              'TwoCuts',
              'Ov5',
              'Ambiguous',
              'Meth_Dep',
              'Not_available',
              'AbstractCut',
              'RestrictionType'),
...

suppliers_dict

Value:
{'B': ('Life Technologies',
       ['MluI',
        'SacI',
        'SalI',
        'BshTI',
        'NcoI',
        'ClaI',
        'DraI',
...

matching

Value:
{'A': 'ARWMHVDN',
 'B': 'CBDGHKMNSRTWVY',
 'C': 'CYSMHBVN',
 'D': 'ABDGHKMNSRTWVY',
 'G': 'GRSKBVDN',
 'H': 'ACBDHKMNSRTWVY',
 'K': 'BDGHKNSRTWVY',
 'M': 'ACBDHMNSRWVY',
...

CommOnly

Value:
RestrictionBatch(['AanI', 'AarI', 'AasI', 'AatII', 'AbaSI', 'AbsI', 'A\
cc16I', 'Acc36I', 'Acc65I', 'AccB1I', 'AccB7I', 'AccBSI', 'AccI', 'Acc\
II', 'AccIII', 'AciI', 'AclI', 'AclWI', 'AcoI', 'AcsI', 'AcuI', 'AcvI'\
, 'AcyI', 'AdeI', 'AfaI', 'AfeI', 'AfiI', 'AflII', 'AflIII', 'AgeI', '\
AgsI', 'AhdI', 'AhlI', 'AjiI', 'AjnI', 'AjuI', 'AleI', 'AlfI', 'AloI',\
 'AluBI', 'AluI', 'Alw21I', 'Alw26I', 'Alw44I', 'AlwI', 'AlwNI', 'Ama8\
7I', 'Aor13HI', 'Aor51HI', 'ApaI', 'ApaLI', 'ApeKI', 'ApoI', 'ArsI', '\
AscI', 'AseI', 'AsiGI', 'AsiSI', 'Asp700I', 'Asp718I', 'AspA2I', 'AspL\
...

NonComm

Value:
RestrictionBatch(['AceIII', 'AhaIII', 'AlwFI', 'AoxI', 'ApaBI', 'ApyPI\
', 'AquII', 'AquIII', 'AquIV', 'Asi256I', 'AspBHI', 'AsuI', 'AvaIII', \
'Bbr7I', 'BbvII', 'Bce83I', 'BcefI', 'BdaI', 'BetI', 'BfiI', 'BinI', '\
BmeDI', 'BmgI', 'BsbI', 'BscAI', 'BscGI', 'BsiI', 'BsiYI', 'Bsp24I', '\
BspD6I', 'BspGI', 'BspLU11I', 'BspMII', 'BspNCI', 'BthCI', 'CauII', 'C\
chII', 'CchIII', 'Cdi630V', 'CdiI', 'CdpI', 'CfrI', 'Cgl13032I', 'Cgl1\
3032II', 'ChaI', 'CjeFIII', 'CjeFV', 'CjeI', 'CjeNII', 'CjeNIII', 'Cje\
P659IV', 'CjePI', 'CjuI', 'CjuII', 'CstMI', 'CviRI', 'DraII', 'DraRI',\
...

AllEnzymes

Value:
RestrictionBatch(['AanI', 'AarI', 'AasI', 'AatII', 'AbaSI', 'AbsI', 'A\
cc16I', 'Acc36I', 'Acc65I', 'AccB1I', 'AccB7I', 'AccBSI', 'AccI', 'Acc\
II', 'AccIII', 'AceIII', 'AciI', 'AclI', 'AclWI', 'AcoI', 'AcsI', 'Acu\
I', 'AcvI', 'AcyI', 'AdeI', 'AfaI', 'AfeI', 'AfiI', 'AflII', 'AflIII',\
 'AgeI', 'AgsI', 'AhaIII', 'AhdI', 'AhlI', 'AjiI', 'AjnI', 'AjuI', 'Al\
eI', 'AlfI', 'AloI', 'AluBI', 'AluI', 'Alw21I', 'Alw26I', 'Alw44I', 'A\
lwFI', 'AlwI', 'AlwNI', 'Ama87I', 'Aor13HI', 'Aor51HI', 'AoxI', 'ApaBI\
', 'ApaI', 'ApaLI', 'ApeKI', 'ApoI', 'ApyPI', 'AquII', 'AquIII', 'AquI\
...