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

Polymer 2Polymer 2 Polymer 3Polymer 3 Polymer 4Polymer 4 Polymer 5Polymer 5 Polymer 6Polymer 6 Polymer 7Polymer 7 Polymer 8Polymer 8Polymer 1Polymer 1 Polymer 9Polymer 9

Enter deposition id [?]: OR CIF File: BrowseBrowse GOGO ResetReset Re-LoadRe-Load

Author Author

Summary Page

Show moreShow moreSelf-reference

Self-reference

New DB reference

Search:

New DB reference

Search:

Enter New Accession code:

Enter New Tax ID:

Version Length Source Organism Tax ID Author’s Annotations From Deposition

1 136 Homo sapiens 9606

Coordinates Coordinates

Select Align Chain ID

Version Length Source Organism

Tax ID Alignment Details

A 1 135 Homo sapiens

9606 Align length (w/ author): 136Similarity (w/o gaps): 0.993 Similarity (w/ gaps): 1.000

B 1 135 Homo sapiens

9606 Align length (w/ author sequence): 136Similarity (w/o gaps): 0.993 Similarity (w/ gaps): 1.000

Reference

Reference

Select Align ID code Version Length Source Organism

Tax ID Alignment Details

UNP:Q9ULI0 (R1)

1 134 Homo sapiens

9606 Similarity (w/o gaps): 0.985Similarity (w/ gaps): 1.000Align length w/ Auth: 136Align range: 952-1085

UNPGB

Norine

UNPGB

Norine

Jasmine April16, 2010

New DB reference

Search:

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 moreShow moreSelf-reference

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 coordinatesorb). Reserve previous sequence processing steps and automatically re-apply to the new coordinates, e.g. global ALA/GLY changeorc). 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:

UNPGB

Norine

UNPGB

Norine