341
Question 11.30
The PlateletWeb can be found at: https://plateletweb.bioapps.biozentrum.uni-wuerzburg.
de/plateletweb.php. For a query, you can, for example, first enter the VASP protein and
have all interactions of VASP calculated. Please also have a look at the tutorial section.
20.12 Life Continuously Acquires New Information in Dialogue
with the Environment
Question 12.1
The link to BLAST is: https://blast.ncbi.nlm.nih.gov/Blast.cgi.
Now test:
Enter random sequence: no hit.
True biological sequence: very small E-value (expected value for a random hit). For
something very common, such as the letter “E” in the database, this value can reach
100,000 or more (if that many E’s were found in an average search of the database). It is
then not a random match, but the probability that this is just a random match is very small
(e.g. less than 10−6, so less than 1 in 1 million). The larger the database, the easier it is to
get random matches, so then the E-value becomes higher.
Question 12.2
The link leads to the protein blast, the database (“non-redundant protein sequences, nr, i.e.
each known protein is contained only once in the database”) is found automatically:
https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins.
(a) Searching in a word: DNA is in the database for protein sequences, James Watson
fails at the J and the O.
(b) Use only meaningful characters: Never use JUZBOX, good counter test if the one-
letter sequence is correct.
(c) Wobble codons denote several nucleotides that are possible at this position, for
example R for purine (A or G) as well as Y for pyrimidine (C or T or in RNA U).
Wobble codons for consensus, here would be optimal to recognize a good and a bad
sequence (at wrong codons, but also at the many NNNNs, perhaps also a polyade
nylation site).
Question 12.3
Check out the https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi page. Go to
the NCBI page on codons. Now you can understand how to translate all the triplets from
nucleic acid sequences to amino acids. There are also variants of the universal code, such
20.12 Life Continuously Acquires New Information in Dialogue with the Environment