[Bioperl-l] New enzymes for RestrictionEnzyme.pm
Steve Chervitz
sac@bioperl.org
Wed, 14 Aug 2002 18:08:27 -0700 (PDT)
For the record, I have no recollection of rebase2perl.pl. Looks like the
comment was written by someone with initials "JA". Not sure who this would be.
Glad that Ryan came through with a functional equivalent.
I'll add the new enzymes to RestrictionEnzyme.pm. I've always thought it would
be neat if this module could obtain its enzyme list by grabbing and parsing
files from the Rebase ftp site. But this project never made it out of the "nice
to have" list. If anyone's interested, be my guest.
Steve
--- Brian Osborne <brian_osborne@cognia.com> wrote:
> Ryan and Steve,
>
> Ryan, thank you for pointing this out, we'll update.
>
> Steve C., you mention a converter script, rebase2perl.pl, in
> RestrictionEnzyme.pm. Do you know where this is and/or can you send it to
> me?
>
> Thanks again,
>
> Brian O.
>
> -----Original Message-----
> From: bioperl-l-admin@bioperl.org [mailto:bioperl-l-admin@bioperl.org]On
> Behalf Of Ryan Brinkman
> Sent: Monday, August 12, 2002 8:13 PM
> To: bioperl-l@bioperl.org
> Cc: sac@bioperl.org
> Subject: [Bioperl-l] New enzymes for RestrictionEnzyme.pm
>
>
> I just had occasion to use RestrictionEnzyme.pm, and noticed the list may
> be out of date (a comment says it was built on a version dated Jan 29 98").
> I think the following entries can be added based on my parsing of the latest
> version of rebase (Aug 01 2002)
>
> 'Acc65I' => 'GGTACC 1',
> 'AceII' => 'GCTAGC 5',
> 'Asp718I' => 'GGTACC 1',
> 'BbeI' => 'GGCGCC 5',
> 'BfrBI' => 'ATGCAT 3',
> 'Bme1580I' => 'GKGCMC 5',
> 'BseBI' => 'CCWGG 2',
> 'BseSI' => 'GKGCMC 5',
> 'BsiLI' => 'CCWGG 2',
> 'Bsp120I' => 'GGGCCC 1',
> 'BssKI' => 'CCNGG 0',
> 'BssNAI' => 'GTATAC 3',
> 'Bst1107I' => 'GTATAC 3',
> 'BstAPI' => 'GCANNNNNTGC 7',
> 'BstKTI' => 'GATC 3',
> 'BstNI' => 'CCWGG 2',
> 'BstOI' => 'CCWGG 2',
> 'BstSCI' => 'CCNGG 0',
> 'Bst2UI' => 'CCWGG 2',
> 'BstZ17I' => 'GTATAC 3',
> 'BthCI' => 'GCNGC 4',
> 'Cfr9I' => 'CCCGGG 1',
> 'ChaI' => 'GATC 4',
> 'Csp6I' => 'GTAC 1',
> 'CviAII' => 'CATG 1',
> 'Ecl136II' => 'GAGCTC 3',
> 'EcoHI' => 'CCSGG 0',
> 'EcoICRI' => 'GAGCTC 3',
> 'EcoT22I' => 'ATGCAT 5',
> 'EgeI' => 'GGCGCC 3',
> 'EheI' => 'GGCGCC 3',
> 'EsaBC3I' => 'TCGA 2',
> 'FatI' => 'CATG 0',
> 'FmuI' => 'GGNCC 4',
> 'FspAI' => 'RTGCGCAY 4',
> 'Hin6I' => 'GCGC 1',
> 'HinP1I' => 'GCGC 1',
> 'Hpy8I' => 'GTNNAC 3',
> 'Hpy99I' => 'CGWCG 5',
> 'Hpy178III' => 'TCNNGA 2',
> 'Hpy188I' => 'TCNGA 3',
> 'Hpy188III' => 'TCNNGA 2',
> 'HpyCH4I' => 'CATG 3',
> 'HspAI' => 'GCGC 1',
> 'KasI' => 'GGCGCC 1',
> 'LpnI' => 'RGCGCY 3',
> 'Mph1103I' => 'ATGCAT 5',
> 'MroNI' => 'GCCGGC 1',
> 'MvaI' => 'CCWGG 2',
> 'NgoAIV' => 'GCCGGC 1',
> 'NgoMIV' => 'GCCGGC 1',
> 'Nli3877I' => 'CYCGRG 5',
> 'NsiI' => 'ATGCAT 5',
> 'OliI' => 'CACNNNNGTG 5',
> 'Ppu10I' => 'ATGCAT 1',
> 'PsiI' => 'TTATAA 3',
> 'Psp03I' => 'GGWCC 4',
> 'PspAI' => 'CCCGGG 1',
> 'PspOMI' => 'GGGCCC 1',
> 'PssI' => 'RGGNCCY 5',
> 'SciI' => 'CTCGAG 3',
> 'SelI' => 'CGCG 0',
> 'SfoI' => 'GGCGCC 3',
> 'Sse232I' => 'CGCCGGCG 2',
> 'TaiI' => 'ACGT 4',
> 'TauI' => 'GCSGC 4',
> 'TscI' => 'ACGT 4',
> 'UnbI' => 'GGNCC 0',
> 'VpaK11AI' => 'GGWCC 0',
> 'XmaI' => 'CCCGGG 1',
> 'XmaCI' => 'CCCGGG 1',
> 'ZraI' => 'GACGTC 3',
> 'Zsp2I' => 'ATGCAT 5',
>
>
>
> Thanks for a great module,
> Ryan Brinkman
> Xenon Genetics Inc.
>
>
>
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=====
Steve Chervitz
sac@bioperl.org
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