Announcing Genome Reconstruction Manager for Phrap (GFP1.2)

Ellen R. Bergeman erb at .NoSubdomain.NoDomain
Mon Apr 14 13:27:26 EST 1997

The Computational Molecular Biology Group at Baylor College of
Medicine is pleased to announce the release of the latest version of
the Genome Reconstruction Manager for Phrap (GFP1.2).

GFP1.2 provides a single user interface within which a user can run
Phred and Phrap on a collection of sequences, look at the resulting
Phrap contigs, examine potential relationships between the contigs,
and access Consed to edit the Phrap contig.

GFP1.2 uses distance and orientation constraints based on sequence
names and user-specified clone sizes to build linked contig structures
called supercontigs and to help verify the correctness of the Phrap
assembly.  GFP1.2 provides the following visual and text reports:

    Supercontig structure - description of supercontigs and the
    constraints which join the contigs

    Closure candidates - list of clones within the maximum clone size
    of the contig end which are not in constraints

    Clone coverage gaps - Regions without constraint coverage 

    Clone coverage closure candidates - list of sequences which are
    not in constraint pairs and are within the maximum clone size of
    the uncovered area

    Single strand gaps - regions of contigs not covered by sequence
    reads on both strands

    Single strand gap closure candidates- list of clones proximal to
    contig regions covered by reads on only one strand

    Orientation violations - list of constrained sequence pairs
    assembled in the incorrect orientation

    Distance violations - list of constrained sequence pairs assembled
    in surprising distances from one another

GFP1.2 has a graphical user interface which displays schematic and
textual reports. A user can choose to look at the information as
schematic reports only, text reports only, or both. The schematic
reports highlight sequences of interest so that they can be examined
in relationship to other sequences in the contigs. Text and schematic
reports can be printed.

GFP1.2 allows the user to specify the minimum and maximum clone insert
sizes to be used in building supercontigs and developing the reports.
The user can also specify clone constraints in a simple text file, to 
allow for exceptional sizes or names within the project.

Additionally, GFP1.2 provides support for reverse complementing of
supercontigs and writing the Phrap consensus sequences to files as
individual contigs and as supercontigs.

More information is available at http://stork.bcm.tmc.edu/gfp or by
contacting Ellen Bergeman  email: erb at bcm.tmc.edu.

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