Reference no: EM132553338

Assignment -

In this assignment help with identifying all possible gene coding sequences from a bacterial genome sequence. This bacterium has been shown to reduce gut inflammation to humans.

To summarise, here is how a bacterial genome "works":

The sequence we give is always the "top" strand and the genes can exist in the "bottom" strand as well. To get the "bottom" strand from the "bottom" strand, you need to 'reverse complement' the sequence (complement by A<=>T and G<=>T and then reverse so first letter is last etc).

In between the genes (note that there are likely to be multiple genes in a genome sequence) is the non-coding space.

Each gene sequence is composed of triplets of A/T/C/G nucleotides called codons (each codon eventually forms an amino acid of a protein).

In bacteria, e ach gene is composed of only one Coding Exon and there are no introns. However, the unique thing about a bacterial genome is that the genes can also overlap: where in one gene might contain the codons: AAT -GCT, the genome might also be read as A-ATG-CT and a different gene might start "within" the same gene.

In bacteria, e ach gene begins with one of the three codons: ATG (usually), GTG (rare) and TTG (very rare) and finishes with a tri-nucleotide TAA, TGA, or more rarely TAG.

These codons, being triplets, means that gene coding sequence is a multiple of three. The non -coding sequence does not have to be a multiple of three and can be any length.

The Stop Codons don't appear anywhere else in the gene but may be present in the non -coding areas.

In the non-coding regions the A/T/C/G letters have a different distribution that in coding sequence since they do not contribute to codons.

ORFs refer to Open Reading Frames which for bacteria is equivalent to putative genes (as bacteria have no introns). They have no stop codons inside the middle of them, they start with a start codon, end with a stop codon but may or may not be real genes.

Note: I'm only interested in the coding sequence (CDS) and not the Untranslated Parts (UTR). The coding sequences will typically be no less than 100 codons (300 nucleotide bases).

Write a report with your solution and an analysis of the method you used (there may be more than one way). Don't forget to tell me how you benchmark your model.

Data access: You will be given 4 FASTA files:

1. Some sample coding sequences that we have already identified as coding genes using other methods,

2. Some sample noncoding sequences

3. A file containing a number of possible Open Reading Frames (ORFs) which are putative genes but could belong to either the coding or non -coding region

4. A 20,000 base pair (20 kb) sequence from the genome sequence.

Attachment:- Assignment & Assignment Data Files.rar