Bacterial Genetics Assignment and Genomics Exercise: http:www'qub'ac'ukmlpagecoursesgenex'htm

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Bacterial Genetics - Assignment and Genomics
Exercise http//www.qub.ac.uk/mlpage/courses/gen
ex.htm

• Aims
• To provide an overview of the development and
  future development of our understanding of
  microbial genetic systems and their evolution
• To initiate a review of the information in the
  course and bring topics together
• To provide a chance for you to practice essay
  writing with assistance in planning and
  construction
• To produce a short report on an on-line sequence
  search
• Your objective
• To write an essay on time with sequence search
  report
• To discuss with your group the seminar topics
• To prepare one OH sheet the topics for discussion
• To gain some help in essay writing and planning

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• Essay Title
• "The expansion of microbial genome and
  metagenomic data in recent years has had a
  profound impact on our understanding of
  microorganisms and their interactions with their
  environment"Deadline LAST DAY OF THIS TERM
• Planning tutorial to be arranged
• 4 to 5 pages of A4 with references cited
• SEMINAR TOPIC
• 4 groups to meet nearer the time to prepare a
  list
• Task to prepare FIVE research
  applications/experiments arising from genome
  sequencing that should be pursued in the area of
  microbiology and the environment in the next 5 to
  10 years
• Prioritise and discuss in final seminar
• One page report on sequence searches from on -
  line exercise
• Add one page of notes on discussion at seminar

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  Bacterial Genetics - Assignment and Genomics
Exercises The BLAST programs (Basic Local
Alignment Search Tools) A set of sequence
comparison algorithms introduced in 1990 that are
used to search sequence databases for optimal
local alignments to a query.
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P value The probability of an alignment
occurring with the score in question or better.
The p value is calculated by relating the
observed alignment score, S, to the expected
distribution of HSP scores from comparisons of
random sequences of the same length and
composition as the query to the database. The
most highly significant P values will be those
close to 0. P values and E values are different
ways of representing the significance of the
alignment.
E value Expectation value. The number of
different alignments with scores equivalent to or
better than S that are expected to occur in a
database search by chance. The lower the E value,
the more significant the score.
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Lambda Ratio To convert a raw score S into a
normalized score S' expressed in bits, one uses
the formula S' (lambdaS - ln K)/(ln 2), where
lambda and K are parameters dependent upon the
scoring system (substitution matrix and gap
costs) employed 7-9. For determining S', the
more important of these parameters is lambda. The
"lambda ratio" quoted here is the ratio of the
lambda for the given scoring system to that for
one using the same substitution scores, but with
infinite gap costs 8. This ratio indicates what
proportion of information in an ungapped
alignment must be sacrificed in the hope of
improving its score through extension using gaps.
We have found empirically that the most effective
gap costs tend to be those with lambda ratios in
the range 0.8 to 0.9.
K A statistical parameter used in calculating
BLAST scores that can be thought of as a natural
scale for search space size. The value K is used
in converting a raw score (S) to a bit score
(S'). lambda A statistical parameter used in
calculating BLAST scores that can be thought of
as a natural scale for scoring system. The value
lambda is used in converting a raw score (S) to a
bit score (S').
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• spQ57997Y577_METJA PROTEIN MJ0577
  gtgi2128018pirA64372... 314 2e-85
• pdb1MJH Structure-Based Assignment Of The
  Biochemical F... 272 1e-72

3. dbjBAA29916 (AP000003) 170aa long
hypothetical protein P... 107 6e-23 4.
spQ57951Y531_METJA HYPOTHETICAL PROTEIN MJ0531
gtgi212801... 91 4e-18 5. gi2622094 (AE000872)
conserved protein Methanobacterium t... 85
4e-16 6. gi2621993 (AE000865) conserved protein
Methanobacterium t... 81 4e-15 7. gi2621194
(AE000803) conserved protein Methanobacterium
t... 80 7e-15