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Chapter 4
The Scaffold Window
clicking fix either calls the parsing method directly to build or rebuild the related index file
or asks for a location where to find the database if it was moved.
Add Database button
This button adds a new database to Scaffold. When selected a file browser appears allowing
the User to point Scaffold to the location where the database he/she wants to load is stored.
Once the FASTA file is selected the Parsing Method Dialog appears.
Edit button
To edit one of the existing databases the User has to select a name from the Loaded
Databases table and click Edit. The Parsing Method Dialog appears.
Delete button
To delete one of the existing databases the User has to select a name from the Loaded
Databases table and click Delete.
After parsing rules are applied or databases are deleted the User can click OK.
Parsing Method Dialog
Figure 4-6: Database Parsing methods dialog
This dialog Box allows the user to select one of the two parsing methods Scaffold uses to
align protein names and accession numbers:
•
Auto Parse— This option provides an automatic way of searching for the optimal
accession numbers between the database and the type of data loaded into Scaffold. It
initially identifies the type of parsing rule that better fits both the data and the selected
database. It then matches the rule protein by protein while ensuring uniqueness. If a
protein does not include the type of rule initially selected, Auto Parse looks for other
rules more compatible with the specific protein accession number and defaults to a more
general accession number if everything fails.
•
Use Regular Expressions— This options opens the Configure Database Parser window
which allows the verification of the protein names and accession numbers alignment for
Scaffold's indexing and parsing. It also gives the possibility to modify the parsing rules
according to the User's needs.
•
How should we identify Decoys?— This box contains typical tags used to label decoy
proteins in a database. When parsing a database that contains decoys the User should
Scaffold User’s Manual
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