Jeffrey Barrick edited this page Nov 9, 2015 · 11 revisions

What is the EFM Calculator?

The Evolutionary Failure Mode (EFM) Calculator is a web-based tool that predicts hypermutable sites in a submitted sequence.

Submitting a Sequence

Upload a sequence for analysis in FASTA, GenBank, or Biobrick XML format. Alternatively, you may paste a sequence into the textbox.

Choosing a Chassis Organism

The EFM Calculator will calculate rates for sequences in two different chassis organisms: E. coli and E. coli RecA-.

Annotated Sequences

If you submit a sequence in a format that supports annotations, such as GenBank and BioBrick XML, you have the option of only searching for hypermutable sites that overlap with annotated regions of the sequence.

Interpreting Results

The results page is split into three sections, the RIP Score, the Results Viewer, and the Results Table.

RIP Score

The Relative Instability Prediction (RIP) score predicts the overall mutational stability of device sequence. A higher score means the sequence is less stable and a lower score means that it is more stable. The RIP score is the sum of the predicted mutation rates for RMDs, SSRs, and BPSs, divided by the mutation rate of BPSs. All repeat sites detected contribute to the RIP score.

Results Viewer

The Results Viewer is a visual representation of the sequence and the scale on the top is in nucleotides. The Results Viewer displays annotated regions, BioBrick part numbers (if applicable), sequence length, RMDs, and SSRs. The bar on the left controls the zoom level, and once zoomed in, the Results Viewer scrolls left and right. Only repeat sites with predicted rates of greater than 1.0E-10 are displayed in the Results Viewer.

Annotated Regions, BioBrick Part Numbers, and Sequence Length

If the user submits a file format with annotations (GenBank or BioBrick XML), the first one or two rows will show those annotations, also referred to as features. Hover your mouse over any of those colored regions and the name of that feature will be displayed. The blue bar shows the length of the whole sequence.

Repeat Mediated Deletions

Repeated Mediated Deletions are represented as sets of block arrows connected by a straight line. They are color coded based on predicted recombination rate. Red indicates a higher predicted rate, and yellow indicates a lower rate. The region connected by a line between block arrows shows the portion of the sequence that is likely to be deleted by recombination. Hovering over an RMD shows its predicted recombination rate.

Simple Sequence Repeats

Simple Sequence Repeats are represented as small rectangles. They are also color coded with the same scale that is used for Repeat Mediated Deletions. Click on an individual SSR to zoom in to the nucleotide level and see the actual series of nucleotides. Hovering over an SSR also shows the individual nucleotides.

The Results Table

The Results Table shows the same information about RMDs and SSRs as the Results Viewer, but in a more precise tabular format. Only repeat sites with predicted rates of greater than 1.0E-10 are displayed in the Results Table. Click on any of the column headers to sort them. The Results Table is divided into the following fields:

Location

Location(s) of SSR or RMD in nucleotides relative to the start of the sequence.

Length

The length of any individual repeating unit. For an SSR the repeating unit would be 'AT' if the whole SSR is 'ATATATAT'. The length in this example is 2. For an RMD, this is the length of an individual homology.

Sequence

The sequence of any individual repeating unit. This is only shown for SSRs. From the example above, 'AT' would be the repeating unit in an SSR of 'ATATATAT'. The repeating units for RMDs tend to be too long to display in a table.

Count

Count refers to the number of times an individual repeating unit occurs. For example, for an SSR that is 'ATATATAT', the individual repeating unit is 'AT' and the count is 4. For RMDs, the count is almost always 2.

Type

Type refers to the type of the repeating element, either a Simple Sequence Repeat (SSR) or a Repeat Mediated Deletion (RMD). An SSR is defined as having a repeating unit length of 15 nucleotides or less. An RMD is defined as having a repeating unit length of greater than 15 nucleotides.

Rate

The predicted mutation rate or recombination rate in events per cell per generation.

Export as CSV

Click the 'Download CSV' button in the top right corner to download the table as a CSV file. Please note, only repeat sites with predicted rates of greater than 1.0E-10 are available for download.

Licensing

The EFM Calculator is for non-commercial use only. The EFM Calculator is licensed under the University of Texas Research License. Please see the github repository for a 'LICENSE.pdf' file.

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