Assignments for Today:

Assignments for Wednesday


Discussion of Take Home Exam 1 (w anwers) (Excel file for extra question) -- Pan Genome and KS Plot slides here

DataBank Searches

Sequence and structure databanks can be divided into many different categories.
One of the most important is:


Supervised databanks with gatekeeper.


  • Swissprot
  • Refseq (at NCBI)

Entries are checked for accuracy.
+ more reliable annotations
-- frequently out of date



Repositories without gatekeeper.


  • GenBank
  • EMBL
  • TrEMBL

Everything is accepted.
+ everything is available
-- many duplicates
-- poor reliability of annotations


One problem in maintaining databanks (supervised and aunsupervised) is "owner ship" of sequences, which in many databanks prevents a continuous update of sequences. Even if errors are detected, they are not easily removed form the databank. E.g. ATP synthase operons in E.coli see

Even species names are often wrongly assigned (slides)

Types of Error in a Databank search

False positives: The number of false positives are estimated in the E-value. The P-value or significance value gives the probability that a positive identification is made in error (same as with drug tests).
Danger: avoid fishing expiditions. If you do 100 tests on random data, you expect one to be positive at the 1% significance level.

You could apply the Bonferroni correction:

The significance level for the individual test is calculated through dividing the overall desired significance level by the number of parallel tests. The hypothesis to be be rejected is that Not all of the individual tests are significantly different from chance. (all in the sense of "at least one"

False negatives: Homologous sequences in the databank that are not recognized as such. If there are only 12000 different protein families, an average a sequence should have (size of the databank)/12000 matches. In other words, the number of false negatives is probably very large.

Discussion: Decay of significance. Can this be corrected?

Addendum to virus and life discussion:

Cellular automata: A'life; John Conway's game of life. [rules: a cell survives if it has two or three living neighbors. A new cell is created on a "dead" square if it has exactly three living neighbors.] The game was popularized by Martin Gardner in Scientific American in 1970.


More information on digital life is at Digital evolution homepage at MSU.
Karl Sims' virtual creatures
are worth a look, movie here.
A similar approach to evolution in silico is here.

A'life not really alive


Go through coral of life ppt slides

What does the term phylogeny mean? Is it compatible with reticulation events?