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
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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