1. User Interface Mock Up for Sequence Processing Jasmine Young, Jawahar Swaminathan The following interface mock ups take into account the functionalities needed to extend the Sequence Editor interface to serve the entire Sequence Processing Module for the Common D&A tool project. The elaborated interface allows the annotators to select: pre-Blast sequence references, self-reference or to redo Blast searches, as well as perform the sequence corrections (original editor UI). This interface represents a key component of the April 2010 D&A deliverable. April 16, 2010 wwPDB Common D&A Tool Project

2. Polymer 2 Polymer 3 Polymer 4 Polymer 5 Polymer 6 Polymer 7 Polymer 8 Polymer 1 Polymer 9 Enter deposition id [?]: OR CIF File: Brows e GO Reset Re-Load Author Summary Page Show more Self- reference New DB reference Search: Enter New Accession code: Enter New Tax ID: VersionLengthSource OrganismTax IDAuthor’s Annotations From Deposition 1136Homo sapiens 9606 Coordinates SelectAlignChain ID VersionLengthSource Organism Tax IDAlignment Details A1135Homo sapiens 9606Align length (w/ author): 136 Similarity (w/o gaps): 0.993 Similarity (w/ gaps): 1.000 B1135Homo sapiens 9606Align length (w/ author sequence): 136 Similarity (w/o gaps): 0.993 Similarity (w/ gaps): 1.000 Reference SelectAlignID codeVersionLengthSource Organism Tax IDAlignment Details UNP:Q9ULI0 (R1) 1134Homo sapiens 9606Similarity (w/o gaps): 0.985 Similarity (w/ gaps): 1.000 Align length w/ Auth: 136 Align range: 952-1085 UNP GB Norine UNP GB Norine Jasmine April16, 2010

3. New DB reference Search: Enter New Accession code: Enter New Tax ID: Above allow annotators to either provide new accession code or new tax id in the text box and then click on “New DB reference Search” button. Have pull down list for databases (UNP, GB, NORINE) for new accession code so that it can search for different databases. Show more Self- reference “Show more” button as shown above: default always display one best match based on author’s taxonomy. when clicking on show more, it will list top 20 best matches. By clicking show more the second time, it will display top 40 best matches (appended new ones to previous list). “Self-reference” button as shown above: when annotator click on this button, system will automatically add self-reference to the data model. “New Coordinates” button: By clicking on this button, there will be a pop up window asking annotators to select one of the below actions: a). Re-run Sequence Alignment on new coordinates or b). Reserve previous sequence processing steps and automatically re-apply to the new coordinates, e.g. global ALA/GLY change or c). Skip sequence processing, retrieve previous saved info such as sequence reference and move on to the next processing step with new coordinates. New Coordinates: System needs to remember original sequence and what it did and the final mapping, and to be able to re-apply tothe new coordinates.When new coordinates arrive, workflow managert checks if sequence 100% match to coordinates and preserved from latest version (batch mode). If ok, apply DBREF to new coordinate and continue. If not, evolk sequence process interface, either re-apply previus sequence selection. Note: UNP GB Norine UNP GB Norine