The Main KeySet Window

This window lists the results of the automatic assembly program. Each item is an assembly of DNA sequencing reads.

After clicking on an item (for example a2), the program opens a Sequence Display window

Sequence Display (fmap) in the assembly package

By default the Sequence Display (fmap) in the assembly package shows the following columns (Appearence is dependent on the presence of the appropriate data in the database).

  • Up Genes
  • Restriction map
  • Scale
  • Down Genes
  • Embl Features
  • Alleles
  • Assembly Tags
  • Alignements
  • Previous Contigs
  • Contigs
  • Trace Assembly
  • Multiplets
  • Brief Identifications
  • Text Features The specialize columns in the assembly sequence display are;.
  • Previous Contigs

  • Contigs

    The Contigs bar has a pop-up menu with the following items
    Flip - flips contig
    Move to - moves contig
    Join to - attempts to join two contigs
    Compair to-
    Fix- automatically changes sequence
    Extend Extremities - attempts to lengthen reads
    Consolidate clips -
    Re-assemble -
    Auto-edit
    Double-Strand
    Clip on Excellent - most stringent clipping
    Clip on Good - stringent clipping
    Clip on Fair - moderately stringent clipping
    Unclip to Max - extend to maximum length
    Repeated 12 mers - show repeated 12 mers from selected contig over the entire project, an exampe is show below.

    The colored bands on the yellow bar at the far left represent the 12 mers. The presence of the additional colored bands on the end of the contig above is a suggestion that the two contigs may be joined.

  • Trace Assembly

    The Trace Assembly lines have a pop-up menu with the following items
    Who am I
    Repeated 15-mer
    Remove Sequence

  • Multiplets

    Multiplets are paired reads from either side of the cloning vector. Lines are created based on the sequence read names. Identical names (excluding the suffix after the last period '.') are joined. Reads separated by more than 1500??? base pairs are in red, reads of the expected size are in light green.

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