2-Protein sequence homology
search.
The EMBL entry U22894 contains the sequence of an amplifiable element AUD1
from Streptomyces lividans. Extract and translate the annotated ORF 4.7
and search for homologous sequences in the protein databases.
Perform the following three database search methods:
-
Blast against protein non-redundant database
-
Fasta against SWISS-PROT
-
Smith-Waterman against SWISS-PROT using the FDF
server or the bioccelerator
at WICC , or locally using PROFILESEARCH.
Use pairwise sequence comparison programs to verify potential homologies.
Questions:
-
Which parts of the hypothetical protein are significantly similar to other
sequences in the database?
-
How many different types of domains does the protein contain?
-
Is the annotation in EMBL "chitinase homolog" correct ?
Hints & Answers:
[BACK]
2 DNA sequence comparisons.
Compare the promoter regions of the mouse and human interleukin-2 receptor
alpha chain genes.
Proceed as follows:
-
Select for each species the sequence entry containing the longest upstream
region.
-
Identify all repetitive elements in each sequence.
-
Locate all homologous sequence regions that exhibit significant pairwise
sequence similarity.
-
Generate alignments of the homologous sequence regions.
Questions:
-
Where are the most conserved sequences located?
-
What percentage of the upstream regions consist of repetitive elements?
-
Do you find significant sequence similarity between repetitive elements?
-
Can you find homologous sequences from other mammalian species using BLAST?
Hints & Answers:
[BACK]