GeneQuest

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Gene Discovery and Sequence Annotation

GeneQuest helps you locate genes, regulatory elements, patterns and structure in your primary DNA sequence. GeneQuest's comprehensive set of analytical methods can be easily applied and manipulated for projects of any size - small, BAC-sized or even larger. You can easily compare sequences with existing genome and EST data using the integrated BLAST feature*, and find out more about related sequences using the integrated Entrez search tool*. GeneQuest also provides annotation and visualization tools so you can document your discoveries for your own use or for publication or submission to public databases.

> GeneQuest Features

    Sequence Entry
  • Import data from many popular file formats
  • Read sequences and features from other Lasergene project files
  • Edit template sequence and share newly created feature through integration with SeqBuilder and other Lasergene modules
  • Download sequences directly from NCBI* or other BLAST servers such as StarBlast using accession numbers, BLAST or text searches
    Gene Finding
  • Predict coding regions using Borodovsky's Markov method
  • Predict intron/exon boundaries using species-specific pattern files for splice sites
  • Align known genes, ESTs or proteins with your sequence
  • Predict where genes start using species-specific pattern files for start sites and transcription factor binding sites
  • Locate ORFs, stops and starts
  • Submit any selected feature, segment, or all of your sequence as a BLAST query*
  • Investigate related sequences using keywords with the integrated Entrez search tool*
    Structure and Composition
  • Display restriction sites
  • Locate direct, dyad and inverted repeats
  • Generate codon usage summaries
  • Simulate agarose gel separations of restriction digests
  • Generate and graph base distribution summaries
  • Plot base frequency and base skew
  • Predict RNA folding
  • Plot localized DNA bending
    Graphical Displays
  • Juxtapose or superimpose related analysis methods or displays
  • View your project at base level and at full overview magnification simultaneously
  • Display data as graphs or boxes indicating a range
  • Choose line colors, fill patterns, and fill colors for all display objects
  • Display features in a variety of shapes and name individual segments

* Requires Internet Connection

» Printable PDF overview for GeneQuest

Screenshot

Apply a variety of methods to the assay surface



Screenshot

Predict RNA folding