Jan 16, 2011 - ApE (A Plasmid Editor) Download, This software is a small, easy to use plasmid editor. I put version 2.0.46 up on the site recently. This version has two new features: 1. An X-ray window activated by pressing the space bar when you have a sequence window active.
Mobile Genetic Elements:
McClintock B. 1951. Chromosome organization and genic expression. Cold Spring Harbor symposia on quantitative biology 16:13-47.
Initial Elucidation of DNA Structure:
Chargaff E, Lipshitz R, Green C. 1952. Composition of the desoxypentose nucleic acids of four genera of sea-urchin. The Journal of biological chemistry 195(1):155-160.
Watson JD, Crick FH. 1953. Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 171(4356):737-738.
Wilkins MHF, Stokes AR, Wilson HR. 1953. Molecular structure of deoxypentose nucleic acids. Nature 171(4356):738-40.
Franklin RE, Gosling RG. 1953. Molecular Configuration in Sodium Thymonucleate. Nature 171(4356):740-741.
High Resolution DNA Structure:
Wing R, Drew H, Takano T, Broka C, Tanaka S, Itakura K, Dickerson RE. 1980. Crystal structure analysis of a complete turn of B-DNA. Nature 287(5784):755-758.
Drew HR, Wing RM, Takano T, Broka C, Tanaka S, Itakura K, Dickerson RE. 1981. Structure of a B-DNA dodecamer: conformation and dynamics. Proceedings of the National Academy of Sciences of the United States of America 78(4):2179-2183.
Initial Sequencing of the Human Genome:
Lander ES, FitzHugh W, Frazier M, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J et al. . 2001. Initial sequencing and analysis of the human genome. Nature 409(6822):860-921.
Venter JC, Holt RA, Yan C, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD et al. . 2001. The sequence of the human genome. Science (New York, N.Y.) 291(5507):1304-1351.
Population Level DNA Sequencing:
Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA, Genomes Project C. 2010. A map of human genome variation from population-scale sequencing. Nature 467(7319):1061-1073.
Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA, Genomes Project C. 2012. An integrated map of genetic variation from 1,092 human genomes. Nature 491(7422):56-65.
Synthetic Genomes:
Annaluru N, Cooper EM, Cai Y, Zeller K, Agmon N, Han JS, Hadjithomas M, Tullman J, Caravelli K, Cirelli K et al. . 2014. Total synthesis of a functional designer eukaryotic chromosome. Science (New York, N.Y.) 344(6179):55-58.
Gibson DG, Moodie MM, Merryman C, Vashee S, Krishnakumar R, Assad-Garcia N, Andrews-Pfannkoch C, Denisova EA, Young L, Qi Z-Q et al. . 2010. Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome. Science 329(5987):52-56.
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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