Comparison Tool

The comparison tool facilitates the temporary collection and comparison of multiple fluorescent proteins across the site. The interface was designed to be similar to the “shopping cart” used by many commercial sites, to provide a familiar experience to the user (note, however, fpbase.org does not sell anything!). The comparison tab slides out from the right side of the page, and is visible on three main internal pages:

1. The main protein table

2. Any individual protein page (pages that begin with www.fpbase.org/protein/)

3. The comparison page itself: www.fpbase.org/compare

Proteins can be added to the comparison tab either by clicking the “Add” button in the comparison tab itself on any given protein page, or by clicking the “+” button in the compare column in any protein row in the protein table at fpbase.org/table. Proteins can be removed from the comparison set by clicking the “X” button next to any protein within the comparison tab. After two or more proteins have been added to the comparison set, the comparison can be accessed by clicking “show comparison” in the comparison tab, or by directly navigating to www.fpbase.org/compare/.

The information displayed in the comparison tab currently includes spectra, excitation & emission maxima, extinction coefficient, quantum yield, brightness, pKa, aggregation, maturation, and lifetime. Furthermore a multiple sequence alignment is performed using MUSCLE (Edgar 2004) and differences between sequences are highlighted. When only two proteins are being compared, the mutations between the first and second protein are calculated using the fpseq package, and displayed below the sequence alignment. Note: the amino acid numbering shown in the mutations is currently based only on the proteins being compared, and is not relative to any ancestral proteins (as is often reported in the literature), nor does it include “lettered” numbering (such as “V1a” in EGFP, often used with amino acid insertions to maintain the position numbering of the ancestral protein).

Directly comparing proteins without using the comparison tab

A set of proteins can also be compared directly by appending a comma separated list of protein “slugs” (the unique protein name identifier found in the URL of each individual protein page) to the comparison URL (www.fpbase.org/compare/). This allows comparisons to be shared via URL, without requiring the recipient of the URL to add each protein to their own comparison set. For instance, to compare the mScarlet proteins in the database: https://www.fpbase.org/compare/mscarlet,mscarlet-i,mscarlet-h/For convenience, the URL corresponding to the current protein comparison always appears towards the top of the page at www.fpbase.org/compare.