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Once you are satisfied with a contig, you can store it in the sequencing project database.
- The archive directory stores the original fragment sequences that you entered into the database with GelEnter. The FAS never modifies the files in this directory.
- The working directory contains the same fragment sequences as the archive, but with all of the gap insertions and edits that were made to assemble the fragments into contigs.
- The consensus directory has a
consensus sequence file for each
contig in the project database.
Each
contig is named after the
left-most fragment in the alignment.
Newly-entered fragments and other
unassembled fragments are also considered
contigs and have a consensus
sequence in the consensus
directory. Because they do
not yet align with any
other contig, they are called
contigs-of-one or
single-fragment contigs.
In addition to these subdirectories, the command directory also contains a copy of each cloning vector specified in GelStart as well as command initializing files for GelEnter, GelMerge, and GelAssemble.
Dr. Roger Staden's pioneering work remains the basis of all work on fragment assembly. GelAssemble comes from the MSE editor written by Dr. William Gilbert. Irv Edelman developed the method of fragment assembly implemented in GelMerge.
We are very grateful to those of you who have taken the time to learn the system and give us useful suggestions. We appreciate your time and hope that implementing your suggestions expresses our gratitude.
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