Biology Reference
In-Depth Information
forward relationship between DNA sequences as they appear in the
database and objects such as “genes” or “exons” or “BAC clones.”
TABLE sequences
UNIQUE KEY (sequence_#)
INDEX KEYS (publication_#, reference_#), (entered_by, entered_date)
sequence_#
REQ
/* accession number for the sequence */
sequence
REQ
/* the sequence itself */
length
REQ
/* redundant, but convenient */
topology
OPT
/* circular, linear, tandem, NULL-unknown */
publication_#
OPT
/* next two give bibliographic source */
reference_#
OPT
entered_date
OPT
/* next two give history of initial entry */
entered_by
OPT
revised_date
OPT
/* next two give history of revision */
revised_by
OPT
DESCRIPTION. The reported sequences. There can be at most one citation, so
it is given here. But the relationship to physical fragments can be many-many,
so that is given in a separate table.
TABLE alignments
UNIQUE KEY (alignment_#, sequence_1, left_end_1, sequence_2)
alignment_#
REQ
/* accession number for alignment */
sequence_1
REQ
/* next three specify fi rst interval to align */
left_end_1
REQ
right_end_1
REQ
sequence_2
REQ
/* next three specify second interval to align */
left_end_2
REQ
right_end_2
REQ
preference
OPT
/* 1 or 2; which one to prefer */
type
OPT
/* confl ict, revision, allele, etc. */
DESCRIPTION. Give an alignment of any number of sequences by specify-
ing pairs of intervals for the line-up. One record of this table gives a pair of
intervals, one from each of two sequences. The set of all records with a given
alignment number gives a complete alignment.
This structure for storing sequence data allows objects of interest to
be reconstructed from the sequences in multiple ways as needed. The
second table shown here—“alignments”—allows different entries in the
“sequences” table to be stitched together in multiple ways by referring
to their sequence accession numbers and coordinates. For example, it
would be possible to create an alignment that spliced sequence A to se-
quence B, or the fi rst 252 base pairs of sequence A to the last 1,095 base
