Gene analysis using molecular biology databases & online
Small tracts of DNA (less than 5 kb) can now be sequenced much more
easily now than ever before. Even students in their formative years of
science (2nd year) are capable of achieving this. This has come
about due to the explosion in technology, knowledge and availability of
kits resulting in cheaper costs and faster data throughput. The complete
sequencing of 15 bacterial genomes in the last two years is testimony to
this. To complement the high throughput genome sequencing projects, development
of data bases and extensive software for data analysis have been developed.
Using such tools in conjunction with molecular biology databases makes
the internet an extremely powerful learning environment for a range of
molecular studies. In addition, it provides useful facts and data for use
in several industries.
The topic is designed to encourage and familiarize you with a range
of online molecular biology tools freely and widely available via the internet
for sequence analysis. For this, you have been given a DNA sequence /courses/bbs6017/sequence.
You will use the online tools and molecular biology databases to answer
a number of questions which are set out below. You should include the following
points as part of your assignment submission:
The first page should include a summary of your answers.
Can you indicate whether the family of enzymes are useful in the food industry.
Explain which food industry and how it is useful.
The summary page should be backed up by attaching hard copies of the supplementary
information you have used to arrive at these answers.
Cite all the references you have used. This should include the URLs as
well as any other references you have sourced.
Identify the primary sequence of the deduced protein expressed by the gene
using 6-frame translation and identify the translation frame.
Does the sequence contain a start codon?
What is the deduced molecular weight and the pI?
If this protein was present in E. coli could you identify its location
on an E. coli 2-D protein map?
Which family / sub-family does it belong to? Mark the conserved amino acids
found in the sequence that identifies it as belonging to the family / sub-family.
Can you determine whether the deduced protein is secreted or cell associated?
Align the deduced protein with 5 of its nearest neighbors. Determine the
percent identity and homology. Differentiate between these two terms.
Proteins are compared on the basis of their domain structures. Can you
explain what the term means? Draw a domain structure model for the deduced
protein and make a comparison with its relatives.
Draw a 3-D model of the deduced protein.