choose schema and create database tables for storing sequences and alignments

[sheridancbio]

• Create database tables for holding sequences. Handle sequence identifiers properly, including a mapping of original sequence identifiers from sequence database source (such as Ensembl or Uniprot) to a set of non-redundant sequences with unique internal identifiers.
• Create database tables for holding alignments between sequence database sequences and pdb sequences. Primary goal is that system can retrieve an amino acid to amino acid mapping between sequence database sequence and pdb structure coordinates (resSeq). Secondary goal is to retrieve information about entire alignment (such as alignment start / end positions and a text representation of the alignment which show matches, mismatches and gaps as shown in a blast hit report.

[pieterlukasse]

This already seems to be there. See the MIDLINE_ALIGN, UNIPROT_ALIGN, PDB_ALIGN fields in table pdb_uniprot_alignment. Maybe the only thing to do is give the UNIPROT_ALIGN field a more generic name?

[sheridancbio]

If the previously created tables fit well, it is not required to reinvent the schema. We probably should compare these schema to Juexin's tables in the project proposal and make sure we are covering what is needed.