Editing/Edited Plasmid Lists in ApE?
Cathal Garvey
Ruediger Trojok
http://gentle.magnusmanske.de/
It is also not totally bug free, but you can add whatever enzyme you
like manually.
> I'm trying to add enzymes to ApE (A Plasmid Editor, see here:http://biologylabs.utah.edu/jorgensen/wayned/ape/) through whatever means
Cathal Garvey
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Nathan McCorkle
Rochester Institute of Technology
College of Science, Biotechnology/Bioinformatics
Anselm Levskaya
there that's free. I actually prefer it to vector NTI. It doesn't do
everything but it does them well and works on every platform. The
Linux version is the source code, and though Tcl is a weird old
language it's not hard to introduce small hacks to it.
Hmm. The manual enzyme addition works fine for me. (OS X version
2.0.30) Just type an arbitrary name in, the cutting spec format is
like this:
EcorI: G^AATTC
MsII: CAYNN^NNRTG
i.e. just 5'->3' IUPAC degenerate alphabet w. "^" denoting the actual
cutsite (I don't think ApE handles type II directionals and the like
explicitly, it just looks for their recognition site, which is all
that matters anyway)
The data files are autogenerated and a bit of a mess.
Strider files are oldschool and nobody uses them anymore. ApE
reads/writes genbank flatfiles, which is what you can download from
NCBI and what vector NTI uses as well. (Biopython et al can also
parse/write them, although the parsers tend to be written by
brain-damaged CS types that care more about formal specification
correctness than actually shutting up and parsing the flatfiles that
exist in the wild. -- i.e. it doesn't parse many older ApE files due
to a trivial difference in the LOCUS header)
Srsly, the file formats used across bioinformatics are a joke. The
reason these braindamaged formats have persisted is that XML was
supposed to save the day... except that XML is an even bigger joke.
(For instance, to retrieve the sequence from an NCBI XML file one
needs to specify this component of the dom tree:
NCBI_xml_result['Bioseq-set_seq-set'][0]['Seq-entry_set']['Bioseq-set']['Bioseq-set_seq-set'][0][u'Seq-entry_seq'][u'Bioseq']['Bioseq_inst']['Seq-inst']['Seq-inst_seq-data']['Seq-data']['Seq-data_iupacna']['IUPACna']
This is braindamaged. What should it be?
NCBI_result['sequence']
)
At some point soon I hope to start making some noise about mapping the
genbank model (or rather, a more practical proper subset of it) into a
JSON format for use by people that, like me, actually design DNA every
day and desperately need human/machine parseable records/models to
work with that aren't overelaborated to the point of parody. (i.e.
Genbank/Biopython provides -5- separate location types: Before, After,
Between, Within, Exact, when for a designer there are just
nucleotides, no allowable uncertainty, and inclusive, explicit slices
to spec ranges)
-a
Lee Nelson
However, the manual-addition system bugs out, not that I'm even sure how it's supposed to work (what's the syntax for the cutting site, etc?).
Try the new alpha version ApE 2.0
Cathal Garvey
I am open to betas, but I usually avoid alpha releases. Particularly when working on a large project.
Thanks for the assistance, everyone. I have switched to gentle, but it's far from perfect: I'm finding it somewhat unstable, and it doesn't expect you to actually want to *write* dna, only to cut and paste things. You can write, but it's not very well implemented IMO. At least it's pointing out all the subtilis-specific enzymes now. Protip: B.subtilis 168 has an endogenous restriction enzyme identical to XhoI. You were warned! :)
Progress continues at a better pace with GENtle though, because real-time annotating of the text sequence with relevant-only restriction enzymes is helping me hack out restriction sites in no time while trying to preserve structure and function. That's not something I could readily do with ApE, even if I had managed to get the restriction enzyme database updated with relevant enzymes.
It's my notion that at some stage in the future we might be able to use B.subtilis to produce secreted restriction enzymes, making purification easy. Because I'm trying to make B.subtilis-genes-only solutions for everything, to allow people to work with this in EU without ridiculous licenses, that means I'm leaving the door open for using endogenous B.subtilis enzymes in the future on this thing. Many of them are isoschizomers of common and popular enzymes:
XhoI (BsuMI), HaeIII (BsuRI), BamHI (BsuB763I), PstI (BsuBI), Eco31I (Bsu537I)... there's a good few more.
Anyway, thanks for the advice re: GENtle and in getting ApE working. I think my install of ApE might simply be unstable. Perhaps it doesn't like being in a Dropbox? Who knows. :)
Website: www.indiebiotech.com
Twitter: @onetruecathal
Nathan McCorkle
"good" or rather, "better" interface would be.