Reference no: EM132250810

1- Download/ install and run Prodigal ( a prokaryotic prediction tool/programming Gene finding Algorithm)

2- Test this Prodigal gene finder on a plasmid of the model organism E. coli O157:H7, The test data can be downloaded from GenBank, accession AB011549.2.

3- Compare the gene prediction with the 'official' annotation on Genbank,

4- And display the results of the comparison as a web page.

5- Write a CGI script to read both the GenBank (reference) annotation and predicted output from Prodigal tool,

6- compare their predicted coordinates and

7- Populate these within an HTML5-compliant template. The output should include summary information at the top, such as:

- Count of genes in the reference annotation

- Count of predicted genes - Count of genes with exact matching coordinates between reference and prediction (5' and 3' agreement)

- Count of genes with 5' agreement but 3' disagreement

- Count of genes with 5' disagreement but 3' agreement - Count of genes predicted with no overlap to a reference gene

-Table showing all gene coordinates of the reference annotation and, beside each, the corresponding (overlapping) predicted coordinates from Prodigal tool.

-Each cell of this table that represents a coordinate from the Prodigal gene predictor should have one of the following class attributes applied to it, 'agrees' or 'disagrees', when compared to the reference coordinates.

-The output should be like the one in the attached output example.png file just replace the Glimmer3 with this Prodigal gene finder.

When performing these comparisons, make sure to:

1- Take into account the strand of the genes involved, else your 5' and 3' agreement calculations will be off.

2- Also be sure to use the CDS features within the genbank file for your comparison, as a single gene in prokaryotes can have multiple CDS as children.

What you will need is:

1-You will need the GenBank entry, from which you can parse out the gene coordinates,

2-And the FASTA version of the DNA molecule itself to be analyzed using Prodigal gene finder.

3-Run it on the E. coli plasmid, saving the results into HTML file.

Attachment:- output.rar