Genome Analysis Software Site

in silico biology, inc.

in silico biology's Products

  • This page introduces the outline of Biosciences software service developed and sold by In silicic Biology Corporation. In silico biology Co., Ltd. develops and sells high-function, easy-to-use, low-cost bioscience software to make more use of biosciences software for more researchers and students.

In silico biology bio software


  • In silico biology Co., Ltd. develops software for research and education that covers a wide field of molecular biology based on nucleic acid (amino acid) sequence analysis. In silico biology's bioscience software has been developed with the utmost importance from users' opinions and requests, and is updated in a very short cycle.
  • There are two kinds of usage license of these software, a floating (dongle) license which can freely transfer a device (PC or Mac) to be used and a device fixed license where the license is fixed to the device

In silico biology development products

(Next generation sequencer data analysis · annotation software)

(Molecular Biology / Sequence Analysis Software)

  • in silico MolecularCloning series
    • Entry Edition: Coming soon.
    • Standard edition
    • Genomics edition
    • Array edition
    • Genome Design Suite (under development) 

(Sequencing / mapping support software)

  • • Metagenome Gamblers Series
    • • Sales termination → Function has been handed over to GenomeTraveler.
    • • Light version
    • • Professional Edition 

(Sequence download software)

  • • Spider series
    • • Taxi spiders: bundled with IMC.
    • • Genome Spider (Eye Spider): It was bundled with IMC.


Products developed at the university (High Speed ​​Comparison Genome Software)

  • • GenomeMatcher (high-speed comparative genomic software) (Microbial · plant secondary metabolite database)
  • • Metabolite DB / Finder (microbial / plant secondary metabolite database)


Imported products

 

  • (Super fast Blast search software)
  • • SLIM Search series (ultra high-speed Blast search software) Suspended

Detailed by product


Genome Traveler


Sales start date: March 28, 2010

  • A new DNA sequencer that can determine a short base sequence in large quantities at high speed has been rapidly spreading and research use is beginning to be started and not only resequencing and mapping but also deNovo assembly of a new sequencer sequence are put to practical use.
  • • This new sequencer is expected to have a larger application field and it can be an important tool for epigenome analysis and various mutation analysis.
  • • Visualize tens of millions of array data.
  • • You can zoom in from mapping results to the reference genome, from the bird's eye view of the entire chromosome to the base sequence.
  • • All existing features on the reference genome sequence can be viewed in parallel with the mapped Short Reads.
  • • In addition, we implemented a function to navigate smoothly between whole genome and whole chromosome as a response to large eukaryotic genome.
  • • There are also three methods for detecting IN / DEL.
  • • Currently, it corresponds to three new sequencer sequence data of Roche / 454 GS FLX, ABI SOLiD, and illumina GA which are already in operation.

In silico Molecular Cloning Series (Standard Edition, Genomics Edition, Array Version)


  • Development Advisor:
    • Nara Science and Technology Graduate School University: It is being developed under the cooperation of Professor Naoki Ogasawara, Professor Shigehiko Kanaya, Professor Kurokawa, Tokyo Institute of Technology.
  • Sales start date: April 1, 2005
  • IMC has great characteristics in that the operation of cloning experiments can be performed on a computer. The cloning function includes basic experiments such as restriction enzyme digestion, PCR primer design, PCR amplification, and ligation. Special data is unnecessary for this execution, and nucleotide sequence data that can be obtained from official databases such as GenBank and EMBL can be cloned as it is. Upon cloning, restriction endonuclease digestion fragments and the terminal forms (sticky ends, blunt ends, etc.) of PCR products are accurately retained, and only the ligation of fragments having the same shape and complementary sequence can be validated . Since Primer information is pasted and stored on the base sequence, it is also useful for Primer management.
  • It is devised so that homology search (NCBI Blast) can be easily executed. Just by reading the annotated base sequence file of the whole genome, the Blast database of all CDS is automatically generated, the homology search is executed by clicking on the feature, the result is graphically displayed, the alignment of the genes Display is also possible. In addition, there are array pattern search, keyword search, feature key search, EC number search, etc. Every operation uses mouse drag-and-clip and many tool buttons so that you can easily use the desired function.
  • Sequencing data in ABI / SCF format can be mapped directly on genomic DNA and alignment with trace waveform can be displayed.
  • When cDNA base sequence file is mapped on genome sequence, it distinguishes between exon and intron and registers it as a feature.
  • From annotation dedicated window, annotation can be executed with simple operation while watching existing annotation, homology search result, base sequence (amino acid) sequence. By using the batch homology search function, you can run homology searches with all of the features in the specified area as queries and automatically post the search results as annotations.
  • The standard version includes basic functions for molecular biology research such as homology search, pattern search function, annotation function as well as cloning function.
  • In addition to the functions of the standard version, the genomics version has added a comparative genome analysis function with a graphical result display.
  • Drawing printing (PDF, PNG, EMF is possible, such as dot plotting, multiple circular genome map, genomic rearrangement map, Venn diagram etc).
  • In the array version, it is excellent in displaying the tiling array experiment results in parallel with existing annotations. It contains all the functions of the genomics version, and the tiling array analysis function is added on it.

License method

  • There are two types of usage licenses for IMC: a floating (dongle) license that allows you to freely transfer licensed devices (PC or Mac) and a fixed license whose license is fixed to the device.

 

University software development bio software


  • We are engaged in sales and technical support of bio-software etc. developed at universities.

Genome matcher


Developer: Tohoku University Graduate School of Life Sciences

Sales start date: May 1, 2008

  • GenomeMatcher is a tool for comparing two DNA sequences. By using this software you can easily obtain a so-called dot plot. We emphasize the utility such as being able to select and reanalyze an arbitrary part on the dot plot with a mouse, to be able to compare while referring to the annotation information, to be able to compare at the base level, to be able to input original annotation information It is made. Many of the results output as text are made on the assumption that it is pasted in a spreadsheet. Since it is possible to export the output image in vector format, it is suitable for preparing materials for presentation.

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