Software Tools :: DNA Sequence Assembly
Sequence assembly (also known as fragment assembly) is the process of
joining overlapping short pieces of DNA to form aligned contiguous sections
(contigs). Usually, raw sequence data comes from the sequencer in the form of
graphical trace files. These can be viewed and converted into textual sequence
files either by the assembly software package itself or by a stand-alone
utility program. The sequence fragments should be processed to remove any
contaminating vector sequences that can interfere with the assembly process;
again this can be done by a stand-alone program or is offered as an option
within many of the assembly systems.
A sequence assembly system typically contains a database to store your
fragments and an editor to allow manual editing of fragments. It keeps track of
the original data as well as the most recently edited version. The fragments
are processed by a sequence assembly engine that computes overlaps between the
sequence fragments and aligns the fragments into contiguous units. There may be
a viewer that lets you see the quality of the alignment and check the read
coverage for each contig, or you may have to print that information in order to
see it.
While there are several assembly systems available on Sunflower (GCG,
Staden, phred/phrap/consed, TIGR), only the GCG Fragment Assembly System is
accessible through the web interface. This software is suitable for
uncomplicated smaller projects; if you have larger projects, contact the CGB
for information about the software available for command-line use.
There are programs available through the web interface that can assist you
in preparing your sequence data for assembly projects: trace viewers that can
convert trace information into sequence files, programs for removing vector
sequences from sequence fragments, and other utilities for processing your
fragments before you enter them into an assembler.
Back to
Sequence Assembly
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