BRM5820 Lab Practical Report And Bioinformatics Assignment, UK

Introduction 

The use of PCR, often followed by an incubation with one or more restriction enzymes underpins much of modern molecular genetics. The practical sessions will have given you information on how to carry out PCR, followed by restriction enzyme digestion and subsequent analysis of the products by electrophoresis. In the computer workshop, you will then be shown how to use DNA sequences to interrogate databases to discover more information about the sequence, where it lies in the genome and how to compare sequences between individuals. 

Assignment 

The assignment will rely on information from the lab practicals and the computer workshop: it is expected that you can be writing the introduction and methodology of the practical section whilst waiting for the computer session. Both components must be submitted as a single document. However, the module coordinator will be available to view drafts of the two sections for feedback at any time prior to submission (within a reasonable timeframe). 

Molecular Genetics practicals: Write a summary report of the results of the practical session beginning with an Introduction section describing the gene used in the practical and its function/links to physical traits (use references). You should then present a brief Methods section explaining what was done in the practical (use scientific journal style), followed by a Results section detailing the outcomes of the experiment – you will also be given some extra genotypic data from the Bioinformatics Workshop to incorporate. From these, you should then present a discussion of the frequency of the different genotypes and individual allelic types identified in the experiment and what implications this might have for a breeding programme within this population. 

Bioinformatics workshop: Following the practical, we sequenced the gene that was isolated via PCR. You will now analyse this sequence using the skills you obtained in the computer workshop. 

Download the file called “sequence.txt” from the Blackboard. Open it with NotePad or MS Word. 

• BLAST your sequence to find its best match in Genbank. - include images of your best hits in the report. 
• What type of sequence is it (e.g., genomic, EST (mRNA))? 
• Find out what chromosome this gene is located in the organism of origin and list the base coordinates. 
• What are the flanking genes of this gene in the cow genome? Are the same flanking genes present in the human genome (if not, record which genes are). 

You are now given a multi-FASTA file containing sequence results for several more individuals from the same population used in the lab practical. Using MEGA, align these and record the number of homozygous dominant, heterozygous and homozygous recessive individuals and record these in your report. Then incorporate these findings with those of the lab practical in terms of allele frequencies as described above.