GeneStudio overview

GeneStudio is a multi-purpose sequence analysis suite.  Currently, GeneStudio includes three sequence analysis components, SeqVerter, an Alignment editor, and a Contig editor.  GeneStudio's modern interface will be familiar to anyone who uses Microsoft Windows software.  All GeneStudio components include drag-and-drop file management using GeneStudio's File window, an Entrez interface for retrieving sequences from the NCBI databases, and a BLAST interface for online similarity searches and hit sequence retrieval.  GeneStudio components are:

SeqVerter is GeneStudio's free sequence file viewer and conversion utility

  • Read and write many popular file formats.
  • Open sequences from multiple files in different formats and combine them into new files.
  • Data viewers include:
    • Sequence file data.
    • Raw sequence file.
    • Trace data, if any.
    • Formatted sequence display for printing or pasting into other applications.

Alignment editor
GeneStudio's Alignment editor provides tools for creating and editing multiple sequence alignments, and phylogenetic analysis.

  • Create alignments using a graphical interface to CLUSTAL W.
  • Edit alignments using the word processor-like editor.
  • In addition, the Alignment editor has a convenient interface to phylogenetic analysis programs, such as TREE-PUZZLEfastDNAml, and selected programs from the PHYLIP package (DNADIST/NEIGHBOR, DNAML, DNAPARS including SEQBOOT and CONSENSE).
  • Data viewers include:
    • Sequence list provides an editable list of open sequences.
    • Pretty view provides a formatted, printable alignment display.
    • An interface to the popular TreeView phylogenetic tree display and editing program is also provided.

Contig editor
The Contig editor provides tools for the assembly and editing of sequences from automatic sequencer files.

  • Automatic trace file trimming.
  • Rapidly locate and edit ambiguous positions with the Ambiguity finder.
  • A translation tool provides editing guidance.
  • Switch between contigs easily using the drop-down contig list.
  • Fold and unfold trimmed ends by dragging the arrow at either end of the sequence.
  • Data viewers:
    • The Contig editor's Viewers window provides displays of the data.
    • The Sequence list is used to select sequences for assembly.
    • The Map view provides a graphical view of contig coverage.
    • The Trace view provides a printable display of the raw trace data.
    • Pretty view provides a formatted, printable display of all sequences in each contig.