Users manual of BioPS system




1 Evaluation of FFA Production Potential:

 1.1  How to determine the free fatty acid (FFA) production potential of a pre-evaluated strain stored in our data repository?

We evaluated the FFA production potential of cyanobacteria with sequenced genomes and stored in our Data Repository. If you would like to see the FFA evaluation of a specific strain, please follow these steps:

  1. Click on Explore Cyanobacteria in the Side Menu on the left.
  2. On the Explore Cyanobacteria page select your strain from the drop down list and click Find.

    Note: if you do not find your strain in the list it means that this strain is not evaluated and is nonexistent in our database. In this case you need to go to Test New Cyanobacteria (please read section 1.3 How to evaluate and test the FFA production potential of a new cyanobacteria strain?)

  3. The evaluation results will appear in the same page.


    In the results section will you will be able to see

    • If the strain is recommended for FFA production or not
    • Species score: this score quantifies the FFA potential of a species. The maximum score among all evaluated species is 1 while the minimum is 0, the higher the score the better the strain.
    • Ranking position: we ranked all the pre-evaluated strains stored in the database based on their species score. The ranking position shows the placement of the strain out of the total number of strains.
    • General Information is shown on a small table such as cell morphology, genome size and total number of proteins.
    • Detailed summary of results: this summary table provides 1/links (proteins present on the genome) to show detailed information of proteins

      1. Proteins present in the organism (positive impact on FFA production)
      2. Proteins present in the organism (negative impact on FFA production)
      3. Proteins required for FFA production and present in the organism
      4. and 2/icon links for

      5. Suggested genetic modifications: insertion/overexpression to increase FFA production
      6. Suggested to be deleted/under expressed to increase FA production
  4. Click on any of the (Proteins hits number) links in any of the tables to get detailed information such as product, start/end location and amino acids sequence of genes present in your strain.

  5. Click on (GeneView) link of a gene to get CyanoBase data such as genomic context and gene ontology of that gene.


  6. To visualize the pathways involved in fatty acid production of this strain, click a link of (Metabolic pathways) under the side menu.

    For example, if you click on Fatty acid biosynthesis, you will view the KEGG pathway of this strain where the present proteins are colored green and the absent proteins colored pink.

    Note, if no strain was selected, only the reference pathway will be seen (without the colored present and absent proteins).



 1.2  How to view the FFA potential of 1/ all pre-evaluated cyanobacteria 2/ specific genus/species stored in our data repository?

To view all of the pre-evaluated cyanobacteria stored in our data repository:

  1. Click on Ranked Cyanobacteria in the Side Menu on the left.

  2. As a result a table will appear with all of the strains ranked from highest to lowest species scores. This score will quantify the biofuel potential of the strain. The maximum score among all evaluated strains is 1 while the minimum is 0, the higher the score the better the strain. The table will also advise on whether the strain is recommended and has high/FFA production potential or not, the results for wet lab experiments for biofuel production (positive, negative, untested), and general information such as cell morphology, genome size and the total number of proteins.


    If you would like to compare a specific genus or species for its FFA production potential:

    1. Type the genus in the specified field or for specificity type in the genus and species.
    2. Click on Search

    For example:


 1.3  How to evaluate and test the FFA production potential of a new cyanobacteria strain?

If your strain is not available in our data repository:

  1. Click on Test New Cyanobacteria in the Side Menu on the left.
  2. Complete the form.
  3. Read the instructions below before uploading the file:
    • You will need to upload the proteome file, which includes the amino acid sequences of the entire predicted set of proteins in genomes, of your strain.  See example  Download example
    • You can obtain the proteome file of your strain from NCBI website. First, search the genome database for your strain. Second, at the top of the page, you will find "Download sequences in FASTA format for genome,protein"; either click directly on the protein link to download the proteome file or click on the genome link to download the genome and reannotate it using INDIGO in order to obtain the proteome file. Similarly, you can download the proteome file from the PATRIC website.
    • Please take into consideration that we will run BLAST as part of our tool, thus; the proteome file of your strain must be in the FASTA format which begins with a short single-line description, followed by lines of sequenced data.
    • This description must include only the Locus tag and the Tag value. The Locus tag is an identifier that is applied to every gene in a genome. The Tag value must be separated from the Locus tag by an underscore ‘_’ (e.g. locus_tag= 'SYPCC7002_00001').

     

  4. Click on Predict
  5.  

  6. Once the progress is completed, BioPS Prediction Results will appear on the screen and contain the following:
    • Species score: This score quantifies the FFA potential of a species. The maximum score among all evaluated species is 1 while the minimum is 0, the higher the score the better the strain.
    • Prediction: there are three categories:“Top ranked”, “Positive” or “Negative” determined based on the species score. To know how the threshold is chosen see paper.
    • Strain recommendation is based on the prediction above.
    • Ranking position: we ranked all the pre-evaluated strains stored in the database based on their species score. The ranking position shows the placement of the strain out of the total number of strains.
    • Detailed summary of results: This summary table provides 1/links (proteins present on the genome) to show detailed information of proteins

      1. Proteins present in the organism (positive impact on FFA production)
      2. Proteins present in the organism (negative impact on FFA production)
      3. Proteins required for FFA production and present in the organism

        and 2/icon links for

      1. Suggested genetic modifications: insertion/overexpression to increase FFA production
      2. Suggested to be deleted/under expressed to increase FA production
    • In addition, you can download the data file containing the locus tags of all the BLASTp hits of FFA impact proteins present on the predicted proteome.
    •  

       

    Note: if you provide your email which is optional,in the form you will receive a summary of your results as well as two attachment files. The first attachment (hitN.txt) contains, the hitN: the number of BLASTp hits per orthologous group (of the FFA impact proteins). The hitN represents the number of hits of all proteins from an OG to the proteome of a species. Note that among all the proteins matched by BLASTp, only the ones with all domains have been used. The second file (locus_tag_hitN.txt) will contain the locus tags of all the BLASTp hits mentioned in hitN.txt


    2 Overview:

     2.1  How to find general information about cyanobacteria?

    If you would like to find general information regarding the evaluated cyanobacteria stored in our database such as Genome size, total number of proteins and cell morphology:

    1. Click on Cyanobacteria in the Side Menu on the left.
    2. For more detailed information click on the provided links to strain related databases such as Cyanobase, KEGG, NCBI genomes and GOLD project
    3.  

    4. If you would like to know about a specific species, or genus, select the category from the drop down list and type the related information.

      Example: Select Species from the drop down list and type 'Prochlorococcus marinus' and click Search, as a result only information on Prochlorococcus marinus species will be provided.

     2.2  How to find proteins impacting FFA production and have been used as a criteria to evaluate cyanobacteria?

    1. Click on Proteins in the Side Menu on the left.
    2. If you would like to look further into the proteins used to evaluate cyanobactia FFA production potential, you can perform four different types of searches based on your interest:

    3.   

       

      1. There are 4 FFA production impact categories: Positive, Negative, Required, and All.

        For example: If you would like to find all genes that positively impact FFA production select from the drop down menu Positive and click Search, you will then be able to see all the positive proteins.

      2.  

      3. You can also search by genes relevant to FFA production by selecting one of the following options: Insertion, Deletion, Overexpression, Underexpression, Present/Required, and All.

        For example if you would like to search for all genes that have been knocked out through genetic engineering to increase fatty acid production choose Deletion from the drop down menu and click Search.

      4.  

      5. You can also view the genes that impact FFA production and are involved in a certain pathway.

        For example if you would like to find all genes involved in fatty acid biosynthesis pathway, select this pathway from the drop down menu. click Search.

      6.  

      7. Use this search if you would like to know if a specific gene is used as a criteria in our tool or if you want additional information about a gene of interest type in the textbox either the gene symbol, its locus tag, its associated UniProt ID, or its related Orthology ID then choose its corresponding category from the drop down menu and click search.

        For example you can type lipA, sll1969, P73372, or K01046 and select the corresponding category gene, locus tag, UniProt ID, or Orthology ID respectively from the drop down menu then click Search.

      8.  

     2.3  How to locate the phylogenetic tree of cyanobacteria?

    If you would like to view the phylogenetic relationship of all pre-evaluated strains stored in our data repository:

    1. Click on Phylogenetic tree in the Side Menu on the left.
    2.