Databases and Systems

2. Explicit declaration by the history in the incoming record. Since NCBI accepts
ASN.l messages directly, the history slot can be used to explicitly declare the
relationship between protein Bioseqs. Of course, these are only allowed if the
nucleic acid Bioseqs of the complex sets containing the proteins are also properly
related. Here, too, a ‘gi’ identifier or its equivalent can be used.
3. Matching by exact sequence identity. This actually happens quite frequently.
4. Matching by exact identity of location on the nucleic acid Bioseq. This can
happen without sequence identity because of a prior error in translation, for example,
caused by using an incorrect genetic code.
Figure 3: Deducing chains for protein ‘gi‘s
Figure 3: Proteins (curly lines) Bioseqs in the new records (on the left) and old records (on the
right) are ordered by their position on the nucleic acid (solid vertical lines). Proteins matched by
one of the above rules are indicated by solid lines, while proteins matched by rule 5 (see the main
text) are indicated by lighted dotted lines. A protein that can not be matched is indicated by the
absence of lines and a question mark.
5. Matching by position in the set of records (Figure 3). Generally, the rule is if
that a protein is bounded by either matched proteins or the end of the DNA sequence,
it is assumed to be in the same chain (be encoded by the same gene). It is realized
that this algorithm will occasionally make mistakes. However, it is usually correct
and the trail of ‘gi’s can be very useful.
Conversion to ‘gi’ Sequence Identifiers
During loading into the ID database, sequence identifiers used as pointers to Bioseqs
are converted to ‘gi’ type sequence identifiers. This allows any subpiece of the
ASN.l message to be used as an independent object by later software, even if
separate from its original Bioseq.
A consequence of this conversion of all other pointer sequence identifiers to ‘gi’
identifiers is that if a record points to a sequence identifier not yet known to ID, the
sequence identifier can not be converted. When such “sought” (currently unknown)
identifiers are defined by having their sequence loaded into ID, the original record is
altered to point to it. This provides some independence from the order of addition of
data to ID and guarantees that all the sequence identifiers that can be converted to
‘gi’ identifiers have been converted, but with computational cost and increased
complexity in the processing code.
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