[ITEM]
20.04.2020

Ape Plasmid Editor Manual

53

ApE documentation (1).doc - ApE A plasmid Editor a Tcl/Tk. School High Point University; Course Title COM 1113; Type. Uploaded By goldchiefer. Pages 42 This preview shows page 1 - 5 out of 42 pages. 12/18/07: We have now started using Wayne Davis' really lovely shareware program ('A plasmid Editor'), which can calculate Gateway recombinations for you: Open sequences for the three entry clones and destination clone (e.g. Using the Genbank-format sequences provided on the wiki).

My dayjob is knitting DNA, and I can recommend ApE as the best outthere that's free. I actually prefer it to vector NTI. It doesn't doeverything but it does them well and works on every platform. TheLinux version is the source code, and though Tcl is a weird oldlanguage it's not hard to introduce small hacks to it.Hmm. The manual enzyme addition works fine for me. (OS X version2.0.30) Just type an arbitrary name in, the cutting spec format islike this:EcorI: G^AATTCMsII: CAYNN^NNRTGi.e. Just 5'-3' IUPAC degenerate alphabet w.

'^' denoting the actualcutsite (I don't think ApE handles type II directionals and the likeexplicitly, it just looks for their recognition site, which is allthat matters anyway)The data files are autogenerated and a bit of a mess.Strider files are oldschool and nobody uses them anymore. ApEreads/writes genbank flatfiles, which is what you can download fromNCBI and what vector NTI uses as well. (Biopython et al can alsoparse/write them, although the parsers tend to be written bybrain-damaged CS types that care more about formal specificationcorrectness than actually shutting up and parsing the flatfiles thatexist in the wild. It doesn't parse many older ApE files dueto a trivial difference in the LOCUS header)Srsly, the file formats used across bioinformatics are a joke. Thereason these braindamaged formats have persisted is that XML wassupposed to save the day. Except that XML is an even bigger joke.(For instance, to retrieve the sequence from an NCBI XML file oneneeds to specify this component of the dom tree:NCBIxmlresult'Bioseq-setseq-set'0'Seq-entryset'Bioseq-set'Bioseq-setseq-set'0u'Seq-entryseq'u'Bioseq'Bioseqinst'Seq-inst'Seq-instseq-data'Seq-data'Seq-dataiupacna'IUPACna'This is braindamaged. What should it be?NCBIresult'sequence')At some point soon I hope to start making some noise about mapping thegenbank model (or rather, a more practical proper subset of it) into aJSON format for use by people that, like me, actually design DNA everyday and desperately need human/machine parseable records/models towork 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 justnucleotides, no allowable uncertainty, and inclusive, explicit slicesto spec ranges)-atechnologiclee26.02.11 14:35. 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. Download xforce keygen autocad 2012 for mac. Perhaps it doesn't like being in a Dropbox? Who knows.:)Website:Twitter: @onetruecathal.

Maxima download mac os x. Download Maxima 5.38 for Mac from our website for free. The Maxima installer is commonly called wxMaxima-0.8.2-Maxima-5.18.1.dmg. Our antivirus check shows that this Mac download is virus free. This free software for Mac OS X is an intellectual property of Maxima Team. The most popular versions of the application are 5.3 and 5.1.

ApE (A Plasmid Editor) 2.0.30 Alpha

ApE is a small, easy-to-use plasmid editor. ApE was developed to be a small, easy-to-use plasmid editor.
ApE Features:
1. Runs in Windows (tested on 98, XP, NT), OS X(10.3, 10.4 and 10.5), and Linux/Unix
2.

ApE is a small, easy-to-use plasmid editor. ApE was developed to be a small, easy-to-use plasmid editor.
ApE Features:
1. Runs in Windows (tested on 98, XP, NT), OS X(10.3, 10.4 and 10.5), and Linux/Unix
2. Highlights restriction sites in the editing window
3. Accurately reflects Dam/Dcm blocking of enzyme sites
4. Highlights text using pre-defined and custom feature libraries
5. Shows translation, Tm, %GC, ORF of selected DNA in real-time
6. Reads DNA Strider, Fasta, Genbank and EMBL files
7. Saves files as DNA Strider-compatible or Genbank file format
8. Highlights and draws graphic maps using feature annotations from genbank and embl files
9. Directly BLASTs selected sequence at NCBI or wormbase
10. Text map shows DNA sequence, translation, and features as text-based graphics
11. Creates graphic restriction maps- linear or circular with features indicated
12. Connects graphic and text features with hyperlink double click
13. Saves graphics as encapsulated postscript or scalable vector graphics
14. Copy and save graphics as Windows metafiles (MS Windows only)
15. Virtual restriction digest
16. Draws pre-defined and user-defined DNA ladders
17. Connects bands to text by double-click
18. Reads ABI sequencing trace files
19. Sequences in ABI traces can be aligned directly to a reference sequence, with the alignment hyperlinked back to te trace.
20. Selects sites matching multiple criteria (union/intersection- cut frequency, site type) in all open windows
21. Selects sites that cut more often in one sequence than another (for snip-SNP detection or diagnostic digests)
22. Has user defined enzyme grouping to distiguish eg. enzymes currently in stock.
23. Allows users to define new enzymes by name and recognition site
24. Imports DNA Strider format files (simple enzyme, site lists) available from REBASEOther Features:
1. Most analysis windows are hyperlinked to their corresponding sequences, includes:
* Graphic Maps
* Text maps
* Virtual Digests
* Alignments (including ABI sequences)
* Silent Sites
* Translation
* Primer Find2. Uses custom feature definition libraries, which allow:
* Quick annotation of sequence
* Quick searching and highlighting of all available primers that you (or others) have that hybridize to a sequence
* Sequence to be annotated and visualized in multiple ways quickly and efficiently
* Graphic maps that show primer binding sites and all interesting sequence features3. Translates sequences with optional DNA alignment
4. Finds potential primers matching user criteria (length, Tm, %GC, self/other complementarity)
5. Aligns two DNA sequences (or any combination of sequence and ABI trace), with the alignment hyperlinked to the original sequence
6. Finds translationally silent restriction sites
7. Draws graphic ORF maps

ApE (A Plasmid Editor) Free Download Information: Free Download 64 is not responsible for software you are downloading nor for details provided about the software 'ApE (A Plasmid Editor) 2.0.30 Alpha' listed here, as the developer can modify information without notifying us. Even if we try to check the files for viruses, we cannot guarantee that they are safe and clean. For your own protection always scan downloaded files for viruses, spyware and malware.

License:Freeware
Size:3.1 MB
Date Added:28 March, 2013
Category:Business / Calculators & Converters
Author:biologylabs.utah.edu

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PopGene.S2 1.0.3380.20651 Beta

PopGene.S2: is a free program to study population genetics. It consists of eight modules, each one directed for one feature of population genetics.Modules are:
1. Allele and genotype frequencies representation
2.

ApE (A Plasmid Editor) Copyright Information: Free Download 64 does not host any 'ApE (A Plasmid Editor)' torrent files or links of ApE (A Plasmid Editor) 2.0.30 Alpha to any free file sharing/upload services including Rapidshare, YouSendIt, SendSpace, DepositFiles, Letitbit, MediaMax, LeapFile, zUpload, DivShare, MediaFire etc. All download links of 'ApE (A Plasmid Editor)' are direct full download from publisher site 'biologylabs.utah.edu' or their selected mirrors. Using warez version, crack, warez passwords, patches, serial numbers, registration codes, key generator, pirate key, keymaker or keygen for Easy Unit Converter 1.2 licence key is illegal and prevent future development of ApE (A Plasmid Editor) by its developer biologylabs.utah.edu.

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[/ITEM]
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20.04.2020

Ape Plasmid Editor Manual

37

ApE documentation (1).doc - ApE A plasmid Editor a Tcl/Tk. School High Point University; Course Title COM 1113; Type. Uploaded By goldchiefer. Pages 42 This preview shows page 1 - 5 out of 42 pages. 12/18/07: We have now started using Wayne Davis' really lovely shareware program ('A plasmid Editor'), which can calculate Gateway recombinations for you: Open sequences for the three entry clones and destination clone (e.g. Using the Genbank-format sequences provided on the wiki).

My dayjob is knitting DNA, and I can recommend ApE as the best outthere that's free. I actually prefer it to vector NTI. It doesn't doeverything but it does them well and works on every platform. TheLinux version is the source code, and though Tcl is a weird oldlanguage it's not hard to introduce small hacks to it.Hmm. The manual enzyme addition works fine for me. (OS X version2.0.30) Just type an arbitrary name in, the cutting spec format islike this:EcorI: G^AATTCMsII: CAYNN^NNRTGi.e. Just 5'-3' IUPAC degenerate alphabet w.

'^' denoting the actualcutsite (I don't think ApE handles type II directionals and the likeexplicitly, it just looks for their recognition site, which is allthat matters anyway)The data files are autogenerated and a bit of a mess.Strider files are oldschool and nobody uses them anymore. ApEreads/writes genbank flatfiles, which is what you can download fromNCBI and what vector NTI uses as well. (Biopython et al can alsoparse/write them, although the parsers tend to be written bybrain-damaged CS types that care more about formal specificationcorrectness than actually shutting up and parsing the flatfiles thatexist in the wild. It doesn't parse many older ApE files dueto a trivial difference in the LOCUS header)Srsly, the file formats used across bioinformatics are a joke. Thereason these braindamaged formats have persisted is that XML wassupposed to save the day. Except that XML is an even bigger joke.(For instance, to retrieve the sequence from an NCBI XML file oneneeds to specify this component of the dom tree:NCBIxmlresult'Bioseq-setseq-set'0'Seq-entryset'Bioseq-set'Bioseq-setseq-set'0u'Seq-entryseq'u'Bioseq'Bioseqinst'Seq-inst'Seq-instseq-data'Seq-data'Seq-dataiupacna'IUPACna'This is braindamaged. What should it be?NCBIresult'sequence')At some point soon I hope to start making some noise about mapping thegenbank model (or rather, a more practical proper subset of it) into aJSON format for use by people that, like me, actually design DNA everyday and desperately need human/machine parseable records/models towork 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 justnucleotides, no allowable uncertainty, and inclusive, explicit slicesto spec ranges)-atechnologiclee26.02.11 14:35. 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. Download xforce keygen autocad 2012 for mac. Perhaps it doesn't like being in a Dropbox? Who knows.:)Website:Twitter: @onetruecathal.

Maxima download mac os x. Download Maxima 5.38 for Mac from our website for free. The Maxima installer is commonly called wxMaxima-0.8.2-Maxima-5.18.1.dmg. Our antivirus check shows that this Mac download is virus free. This free software for Mac OS X is an intellectual property of Maxima Team. The most popular versions of the application are 5.3 and 5.1.

ApE (A Plasmid Editor) 2.0.30 Alpha

ApE is a small, easy-to-use plasmid editor. ApE was developed to be a small, easy-to-use plasmid editor.
ApE Features:
1. Runs in Windows (tested on 98, XP, NT), OS X(10.3, 10.4 and 10.5), and Linux/Unix
2.

ApE is a small, easy-to-use plasmid editor. ApE was developed to be a small, easy-to-use plasmid editor.
ApE Features:
1. Runs in Windows (tested on 98, XP, NT), OS X(10.3, 10.4 and 10.5), and Linux/Unix
2. Highlights restriction sites in the editing window
3. Accurately reflects Dam/Dcm blocking of enzyme sites
4. Highlights text using pre-defined and custom feature libraries
5. Shows translation, Tm, %GC, ORF of selected DNA in real-time
6. Reads DNA Strider, Fasta, Genbank and EMBL files
7. Saves files as DNA Strider-compatible or Genbank file format
8. Highlights and draws graphic maps using feature annotations from genbank and embl files
9. Directly BLASTs selected sequence at NCBI or wormbase
10. Text map shows DNA sequence, translation, and features as text-based graphics
11. Creates graphic restriction maps- linear or circular with features indicated
12. Connects graphic and text features with hyperlink double click
13. Saves graphics as encapsulated postscript or scalable vector graphics
14. Copy and save graphics as Windows metafiles (MS Windows only)
15. Virtual restriction digest
16. Draws pre-defined and user-defined DNA ladders
17. Connects bands to text by double-click
18. Reads ABI sequencing trace files
19. Sequences in ABI traces can be aligned directly to a reference sequence, with the alignment hyperlinked back to te trace.
20. Selects sites matching multiple criteria (union/intersection- cut frequency, site type) in all open windows
21. Selects sites that cut more often in one sequence than another (for snip-SNP detection or diagnostic digests)
22. Has user defined enzyme grouping to distiguish eg. enzymes currently in stock.
23. Allows users to define new enzymes by name and recognition site
24. Imports DNA Strider format files (simple enzyme, site lists) available from REBASEOther Features:
1. Most analysis windows are hyperlinked to their corresponding sequences, includes:
* Graphic Maps
* Text maps
* Virtual Digests
* Alignments (including ABI sequences)
* Silent Sites
* Translation
* Primer Find2. Uses custom feature definition libraries, which allow:
* Quick annotation of sequence
* Quick searching and highlighting of all available primers that you (or others) have that hybridize to a sequence
* Sequence to be annotated and visualized in multiple ways quickly and efficiently
* Graphic maps that show primer binding sites and all interesting sequence features3. Translates sequences with optional DNA alignment
4. Finds potential primers matching user criteria (length, Tm, %GC, self/other complementarity)
5. Aligns two DNA sequences (or any combination of sequence and ABI trace), with the alignment hyperlinked to the original sequence
6. Finds translationally silent restriction sites
7. Draws graphic ORF maps

ApE (A Plasmid Editor) Free Download Information: Free Download 64 is not responsible for software you are downloading nor for details provided about the software 'ApE (A Plasmid Editor) 2.0.30 Alpha' listed here, as the developer can modify information without notifying us. Even if we try to check the files for viruses, we cannot guarantee that they are safe and clean. For your own protection always scan downloaded files for viruses, spyware and malware.

License:Freeware
Size:3.1 MB
Date Added:28 March, 2013
Category:Business / Calculators & Converters
Author:biologylabs.utah.edu

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If you could look 1 year ahead, would you want to see? Startup Product Manager will help you calculate your business plan. Fine-tune cost-profit parameters as you want. See results graphically displayed over 48 months. Various simulations included.

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Truck and container loading software. Easy to learn. Unlimited load plan calculations, manual load plan adjustments. Real 3D visualization. Imperial (US) and Metric units. Weight distribution calculation. Available online. Full ver. 10 days for free!

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PopGene.S2 1.0.3380.20651 Beta

PopGene.S2: is a free program to study population genetics. It consists of eight modules, each one directed for one feature of population genetics.Modules are:
1. Allele and genotype frequencies representation
2.

ApE (A Plasmid Editor) Copyright Information: Free Download 64 does not host any 'ApE (A Plasmid Editor)' torrent files or links of ApE (A Plasmid Editor) 2.0.30 Alpha to any free file sharing/upload services including Rapidshare, YouSendIt, SendSpace, DepositFiles, Letitbit, MediaMax, LeapFile, zUpload, DivShare, MediaFire etc. All download links of 'ApE (A Plasmid Editor)' are direct full download from publisher site 'biologylabs.utah.edu' or their selected mirrors. Using warez version, crack, warez passwords, patches, serial numbers, registration codes, key generator, pirate key, keymaker or keygen for Easy Unit Converter 1.2 licence key is illegal and prevent future development of ApE (A Plasmid Editor) by its developer biologylabs.utah.edu.

Categories

Top Downloads

New Downloads

  • home
  • latest
  • popular
  • submit
  • bookmark
  • rss feeds
  • link to us
  • privacy