Fitness BLAST Example

For a specified protein sequence, Fitness BLAST shows homologs that have fitness data, as identified by usearch.

Short Results

The short result shows up to two hits. It always includes the top hit with fitness data (if there is one). It may show another hit if the top hit does not have a significant phenotype or strong cofitness but another hit does.

E. coli gene	Short fitness BLAST result
uvrC
yqiB
csrA

Detailed Results

The table result shows all of the homologs of the gene in the organisms that we have fitness data for (up to a limit of 50). Here is the table for uvrC from E. coli.

The fitness field gives the range of fitness values that were observed, so that you can see if the gene has any strong phenotypes. Statistically significant values are in bold. The cofit field shows the highest cofitness value, so that you can see if the gene's fitness pattern is similar to that of another gene.

Incorporating Fitness BLAST into a web page

You can see an example of Fitness BLAST incorporated into another web site at the MicrobesOnline gene info page. To incorporate Fitness BLAST into your own HTML page, all you need is a protein sequence and a few lines of javascript. The ingredients are:

Two script tags that load the javascript libraries from fit.genomics.lbl.gov/d3js/d3.min.js and fit.genomics.lbl.gov/images/fitblast.js
A div tag named "fitblast" (or whatever name you choose)
A script tag that uses the fitblast_load_short() javascript function to load the short-form results into the specified div tag given the specified Fitness BLAST server and a protein sequence. (Or use fitblast_load_table() with the same arguments to load the table instead.)

and here is a concrete example:

<script src="https://fit.genomics.lbl.gov/d3js/d3.min.js"></script>
<script src="https://fit.genomics.lbl.gov/images/fitblast.js"></script>
<div id="fitblast"></div>
<script>
  fitblast_load_short("fitblast", "https://fit.genomics.lbl.gov/",
      "MKILVIGPSWVGDMMMSQSLYRTLKARYPQAIIDVMAPAWCRPLLSRMPEVNEAIPMPL");
</script>

You can also look at the HTML source for this page. If you use fitness_load_table(), note that the table it creates will be of class fitblast, so you set table.fitblast styles in cascading style sheets to modify how it is formatted.

Alternatively, to have Fitness BLAST return formatted HTML, use URLs like this:

https://fit.genomics.lbl.gov/cgi-bin/seqservice.cgi?html=1&seq=MSSLQRIVLIDTHLPGVVELALDGHTNICGTNASGKTTLQRLVPVFYGEYPSRVVPSTRDSFERWYLPHDSSYIIYEYRRGDGMLYQAVLSSNGDGKGISYRFIAKGFELDDYVKARNGDS

Fitness BLAST for Genomes

As an alternative, you can pre-compute best hits for all genes in a genome at once (link).

Developed by Morgan Price. Please report any errors to Morgan.