The following box allows you to enter a valid email address. Once your BLAST job is completed, you will receive an email notification with a link that directs you to the phylogenetic profiling table.

As an example, this tutorial tries to identify the conservation of a gene cluster involved in Phosphate Transport and Regulation (a cluster of 5 genes in Caulobacter crescentus CB15, an Alphaproteobacteria) in other stalked and non-stalked Alphaproteobacteria (like Maricaulis maris, Jannaschia sp., Silicibacter sp., Rhizobacterium etli, etc.)

From the list of available genomes, select the organisms of your choice, that you wish to BLAST and visualize your query sequences against. You can select/unselect the organisms by using the Add/Remove controls. Alternatively, if you choose to select all the available genomes, you may do so by using the 'Select all genomes' radio button.

Following the selection step, submit your query sequence(s) either via the text-box (copy-paste a set of sequences) or by uploading a file (data must adhere to the FASTA file format).

Click on 'BLAST' to submit your job by accepting the default parameters or configure your BLAST job by modifying the Advanced Parameters according to your needs. You are allowed to modify various parameters like Word Size, Threshold score for extending hits, Effective length of database, etc.

On completion of the BLAST job, you are presented with a phylogenetic profiling table that displays the list of chosen organisms in a table, against a count of the hits of each query sequence against each organism. This list allows you to choose the organisms which you would like to visualize.

By default, the table is sorted by clustering score, i.e. it is first sorted by the number of matched distinct query sequences and then sorted by the total number of matched query sequences. Also, users can sort the table in alphabetic order of species names or by individual query sequences

After choosing the organisms from the list, Proceed to the visualization page.

Depending on the number of organisms chosen, the visualization page may take a considerable amount of time to draw the image. Once drawn, you are provided with a wide array of buttons to navigate through each the image.

Mouse over the image to learn more about each element.

As you can see in the image below, the cluster of 5 genes is seen to be conserved completely in 1 and partially in 2 out of the 3 organisms (Rhizobium etli CFN42, Jannaschia sp. CCS1, and Maricaulis maris MCS10)

An image w.r.t a particular organism, is independent of the other images and can thus be navigated through as an independent entity. Each image is equipped with buttons to pan left/right, zoom in/out, choose a particular range and filter the hits based on a particular e-value.

In an image, the black bar corresponds to the genome, the tracks identified in green correspond to the annotation information derived from the GFF files, and last set of tracks correspond to the query sequences. Based on the magnification level, relevant information(such as GI numbers, locus, etc.) w.r.t to the query or the hit regions is displayed alongside the arrows.

In each image, you can mouse-over a particular query sequence or hit region. This provides you with snippets of information relevant to the particular query or hit region. On click, a new page opens up, providing you with more detailed information as follows:

• Query sequence information (name, sequence against which it showed similarity, full BLAST alignment)

  

• Hit sequence information (organism name, description, locus, synonym and the nucleotide & amino acid sequence.)