Bioinformatics atgeneXplain GmbH         Introducing IMC
geneXplain GmbHProducts   Bioinformatics and systems biology: geneXplain platform   Bioinformatics and NGS: IMC and Geno...
Cheminformatics and Systems Biology   geneXplain platform    ◦ Collection, storage and analysis of experimental data    ◦...
geneXplain GmbHProducts   Bioinformatics and systems biology: geneXplain platform   Bioinformatics and NGS: IMC and Geno...
Contents   in silico molecular                    Search and    biology                                 customization   ...
in silicoMolecular Biology  Major functions of IMC         info@genexplain.com |           www.genexplain.com    6
General InformationIMC comes in three different editions and features threemajor in silico experiment areas: Cloning (Sta...
IMC-SE, -GE, -AECloningThe "Cloning" menu lists a number of possibleactions for in silico molecular cloning experiments.In...
IMC-GE, -AEGenome AnalysisThe "Genome Analysis" menu is filled with functions fromstatistics to visualization to working w...
IMC-GE, -AEGenome AnalysisA special feature of the             genomeanalysis functionality is the        genomerearrangem...
IMC-AEArray AnalysisThe "Array Analysis" menu contains all functionsnecessary for the creation and analysis of arraydata: ...
Summary   in silico molecular cloning            Genome analysis      options include PCR,              features translati...
Search andCustomization Additional features of all IMC editions         info@genexplain.com |           www.genexplain.com...
General InformationIn addition to thepreviously introducedmajor functions, IMCalso stands out fromthe crowd for its: sear...
Search FunctionsThe "Search" menu offers thepossibility to search for keywords,patterns (short sequences, seeexample below...
VisualizationIt is possible to access different viewsof your sequence files via the "View"menu, including circular genome ...
Feature CustomizationIt is possible tochange form andcolor of every kindof feature, adjusttheir position onthe feature map...
Interface CustomizationThe toolbox of IMC is customizable as well.Remove the buttons you dont need to focuson your favorit...
Summary   Customization of features     Search for keywords and     and the feature map.          sequence patterns.      ...
Why You Should       Try IMCAdvantages of the Software       info@genexplain.com |         www.genexplain.com    20
Advantages of IMC   IMC offers a wide range of functions to work with whole    genome data, from in silico cloning to gen...
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in-silico Molecular Cloning

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IMC is a renowned software package developed by in silico biology, inc. in Yokohama, Japan. It is well established on the Japanese market where it became very popular among hundreds of customers. GeneXplain has carefully selected this program package for its portfolio because of its rich functionality, proven reliability, excellent maintenance policy by the original providers and its perfect fit to geneXplain’s strategic aims. Being introduced to the Japanese market 6 years ago, it is a mature and approved product that customers outside Japan can now also benefit from.

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in-silico Molecular Cloning

  1. 1. Bioinformatics atgeneXplain GmbH Introducing IMC
  2. 2. geneXplain GmbHProducts Bioinformatics and systems biology: geneXplain platform Bioinformatics and NGS: IMC and GenomeTraveler Cheminformatics: PASS, PharmaExpert, GUSAR info@genexplain.com | www.genexplain.com 2
  3. 3. Cheminformatics and Systems Biology geneXplain platform ◦ Collection, storage and analysis of experimental data ◦ Network clustering and search for master regulators ◦ Graphical programming of workflows ◦ Possibility to write new scripts and add-ons PASS and PharmaExpert ◦ Qualitative biological activity prediction for libraries of chemical compounds ◦ Drug-drug interactions and identification of most promising candidates GUSAR ◦ Quantitative biological activity prediction for libraries of chemical compounds ◦ (Q)SAR model building info@genexplain.com | www.genexplain.com 3
  4. 4. geneXplain GmbHProducts Bioinformatics and systems biology: geneXplain platform Bioinformatics and NGS: IMC and GenomeTraveler Cheminformatics: PASS, PharmaExpert, GUSAR info@genexplain.com | www.genexplain.com 4
  5. 5. Contents in silico molecular  Search and biology customization ◦ General information ◦ Search functions ◦ Cloning ◦ Visualization ◦ Genome analysis ◦ Feature customization ◦ Array analysis ◦ Interface customization  Why you should try IMC info@genexplain.com | info@genexplain.com | www.genexplain.com www.genexplain.com 5
  6. 6. in silicoMolecular Biology Major functions of IMC info@genexplain.com | www.genexplain.com 6
  7. 7. General InformationIMC comes in three different editions and features threemajor in silico experiment areas: Cloning (Standard, Genomics and Array Edition) Genome analysis (Genomics and Array Edition) Array analysis (Array Edition)The software accepts a range of sequence files: GenBank, EMBL, GPFF formats FastA format Amino acid files authorship and copyright by in silico biology, Inc., Yokohama, Japan distributed by the geneXplain GmbH info@genexplain.com | www.genexplain.com 7
  8. 8. IMC-SE, -GE, -AECloningThe "Cloning" menu lists a number of possibleactions for in silico molecular cloning experiments.Included are all necessary functions for: ◦ PCR (including gel electrophoresis of results) ◦ Ligation and sequence editing ◦ Restriction enzymes and digestion (example below) info@genexplain.com | www.genexplain.com 8
  9. 9. IMC-GE, -AEGenome AnalysisThe "Genome Analysis" menu is filled with functions fromstatistics to visualization to working with sequences: ◦ Translation ◦ Annotation ◦ EST and trace mapping ◦ Homology searches ◦ Dot plot, Venn diagram (examples below), KEGG pathways info@genexplain.com | www.genexplain.com 9
  10. 10. IMC-GE, -AEGenome AnalysisA special feature of the genomeanalysis functionality is the genomerearrangement map. With it, you cancompare the positions of loci indifferent genomes as seen in theexample below. info@genexplain.com | www.genexplain.com 10
  11. 11. IMC-AEArray AnalysisThe "Array Analysis" menu contains all functionsnecessary for the creation and analysis of arraydata: ◦ Probe design (example below) ◦ Import of probe and array data ◦ Statistics and peak detection ◦ Two expression graphs and clustering info@genexplain.com | www.genexplain.com 11
  12. 12. Summary in silico molecular cloning Genome analysis options include PCR, features translation, restriction and ligation of annotation, homology sequences. searches and more. IMC offers a range of functions for in silico molecular biology. Array analysis offers IMC comes in three probe design, data different editions: import, peak detection standard, genomics and and more. array. info@genexplain.com | www.genexplain.com 12
  13. 13. Search andCustomization Additional features of all IMC editions info@genexplain.com | www.genexplain.com 13
  14. 14. General InformationIn addition to thepreviously introducedmajor functions, IMCalso stands out fromthe crowd for its: search, customizability and visualization options. info@genexplain.com | www.genexplain.com 14
  15. 15. Search FunctionsThe "Search" menu offers thepossibility to search for keywords,patterns (short sequences, seeexample below) and classifications. info@genexplain.com | www.genexplain.com 15
  16. 16. VisualizationIt is possible to access different viewsof your sequence files via the "View"menu, including circular genome maps(example below). These are, of course,also fully customizable. info@genexplain.com | www.genexplain.com 16
  17. 17. Feature CustomizationIt is possible tochange form andcolor of every kindof feature, adjusttheir position onthe feature mapand activate ordeactivate labels.Additionally, thelayout of the mainfeature map is alsofully adaptable. info@genexplain.com | www.genexplain.com 17
  18. 18. Interface CustomizationThe toolbox of IMC is customizable as well.Remove the buttons you dont need to focuson your favorite functions! info@genexplain.com | www.genexplain.com 18
  19. 19. Summary Customization of features Search for keywords and and the feature map. sequence patterns. Thanks to all the little things, IMC is a very flexible tool. Visualize your sequence Flexible selection of in different formats. function buttons. info@genexplain.com | www.genexplain.com 19
  20. 20. Why You Should Try IMCAdvantages of the Software info@genexplain.com | www.genexplain.com 20
  21. 21. Advantages of IMC IMC offers a wide range of functions to work with whole genome data, from in silico cloning to genome and array analysis. The program can read a number of sequence file formats. There are three different editions of IMC: you only pay for the functions you need! Layouts in IMC are fully customizable. The software is already well-established on the Japanese market and is updated regularly. You can download a free two-week trial version of IMC at http://www.genexplain.com/imc info@genexplain.com | www.genexplain.com 21

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