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IMC Overviews

This page is the home page of IMC (in silico MolecularCloning).

Features of in silico MolecularCloning


Advisors for the product development

Development of IMC is conducted by Professor Naotake Ogasawara of Nara Institute of Science and Technology and Professor Ken Kurokawa of Tokyo Institute of Technology.

Development Policy

  • IMC is a sequence analysis software of the genome age.
  • The operation of IMC is based on the central dogma of molecular biology.
  • IMC is frequently updated, namely once in a week.
  • IMC promptly reflects the requirements of its users,

Features of IMC

User License of IMC

Trial Use

Operation Manuals of IMC

  • IMC's manual can be downloaded after installation of IMC program.

Functions of IMC


Handling of Annotated DNA and Amino Acid Sequences


  • Fast Reading of large DNA sequence files
  • Exporting of Features and Sequences in CSV
  • Generation of GenBank and EMBL format files
  • Generation of FastA(Single, Mupltiple) format files with flexible definition line
  • Generation of batch DDBJ submission format files
  • Direct Reading compressed sequence files and expansion of each entries onto the taxonomy tree
  • Easy DNA sequence fetching using TaxiSpider

Cloning in silico


IMC provides typical cloning experiments on a computer. No special data is required but only annotated GenBank or EMBL sequence files are used for the experiments. Namely, any two GenBank files can be ligated together with their annotation on. Cloning maintains annotation on these sequences during restriction enzyme digestion, PCR amplification and ligation. The resulting ligation files are generated in GenBank or EMBL format. Primer info can be mapped on the genome and this function is useful to manage numerous primer sets to be easy to find status.

  • Restriction Enzyme Digestion
  • PCR Primer Design
  • PCR Amplification
  • Primer Management
  • Ligation
  • Plasmid Map
  • Gel Electrophoresis

Drawing and Operation of Feature Map


IMC has various customization facilities on the Main Feature Map.

  • Drawing of the Main Feature Map
  • Customization of the Map
  • Flexible Feature Layout Style
  • Regitration of User-Defined Feature Keys
  • Endless scrolling around a circular DNA sequence
  • Fast Zooming and Scrolling
  • Feature Map's Co-moving with GenBank/EMBL File Viewer
  • Content Profile Lanes such as GC Content, GC Skew, TESTCODE profie of Fickett Algorithm
  • Import and profiling of any genome position-specific numerial data files

Feature Mapping


Import of Result files of Gene Detection Software

  • Glimmer
  • GeneScan
  • MetaGeneAnnotator(MGA)
  • AUGUSTUS
  • tRNAScan-SE
  • RNAmmer

Import of feture files

  • BED
  • CSV
  • GFF
  • GTF
  • JSNP, dbSNP
  • XanaGenome
  • GenomeGAMBLER

Importing and Mapping of result files of homology searches

  • Blast resutl files

Sequence Mapping


  • Mapping of EST(cDNA) sequences on the reference genome sequences
  • Mapping of ABI/SCF files on the reference genome sequence files.
  • Mulitiple Trace Alignment

Sequence Analysis


  • DNA translation to amino acids
  • Detection of Start and Stop codon candidates
  • Generation of Codon and Amino Acid Usage Tables
  • ORF Extraction
  • Reverse complimentary operation

Search Functions


  • Sequence Pattern Search(Nucleotide and Amino Adid) on CDS or intergenic regions
  • Keyword Search
  • Feature Key Search
  • EC Number Search
  • Automated Homology Search (between the Main Feature Map and the Reference Genome Maps, against locally created sequence databases, against NCBI using NetBlast)
  • Create Databases for Homology Search
  • Automated Batch Homology Search
  • Automated Tranfer of Annotion
  • Multiple Alignment of DNA and amino acid
  • Phylogentics Tree

Manual and Automated Annotation


The Annotation window provides useful tools for manual annotation.

  • Automatic Transfer of Annotation
  • Homology Searchy Result Saving and Referring

Comparative Genome Analysis(Genomics and Array Editions)


Comparative Genome Analysis features are implemented on the IMC Genomics Edition and IMC Array Edition.

  • Multi-genome Alignment Feature Map
  • Homology Search between Chromosomes
  • Feature Alignment
  • Circular Genome Map
  • Dot Plot
  • Genome Rearrangement Map)
  • Venn Diagram)
  • Detection of Repetive Sequeces
  • Detection of Unique Regions between Related Genome Sequences

Tiling Array Analysis(Array Edition)


IMC Array Edition provides a high-resolution profiling of tiling array data comparing with existing annotation about the genomes. IMC Array Edition supports arrays of Affymetrix ,Agilent and Nimblegen.

  • Infinite number of array profiles are visible in parallel with aligning with the existing annotation
  • Data correction of array expression intensities
  • Between-Arrays Operators, saving of operation results
  • Data Conversion from Probe-level to Gene-level expression intensities
  • Clustering about gene-level expression intensities
  • Peak detection along the profiles

Utilities


  • Automated cheking of later version and downloading from ISB download site
  • Automated downloading of IMC help file

 

 

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