Course Goal
Know and use
computational
biology to
predict the
evolutionary
relatedness
and function of
proteins
Learning
Objectives
- use
computation
biology
databases,
such Blast,
SwissPro, and
Flybase to
identify
homologues
and predict
putative
function of a
protein
Cognitive Level
-application
-interpretation
-evaluation
Summative
Assessment
Upload Final
Annotation
Report of an
unknown
Drosophila
genomic
sequence
including all
gene features,
predicted
proteins, and
functional
homologues
Cognitive Level
-application
-interpretation
Formative
Assessment
You have been
assigned the
following
Drosophila
melanogaster
protein, SWA1
(swallow).
Using the
listed
databases,
completely
annotate the
gene and
confirm the
predicted
function based
on known
homologs.
Blooms Category: Application, Analysis and Evaluation
You have been assigned the following Drosophila melanogaster, SWA1 (swallow). Using
Flybase, Genbank, NCBI blast, and SwissPro and Genescan complete the following:
a.
Retrieve the genomic sequence as a FASTA file (store in Sequence Folder on the
Wiki)
b. Using NCBI blast perform a tblastx search on your gene sequence. Capture and
store on the Wiki.
c. Determine the top ten hits based on E value. Report these on your data sheet.
d. Determine the first related species not in Drosophila. Report this on your data sheet.
e. Using SwissPro analyze the protein sequence of your gene for functional domains,
binding motifs, structural features. Report your findings on your data sheet.
f. Determine secondary structural features of your protein.
g. Using Genescan, predict the genomic structure of your gene. Include all exons,
introns and splice sites in the model. Paste link up on the Wiki.
In 1-2 pages report the putative function of your protein based on your interpretation of your
results from the above modeling programs. Include potential irregularities in your predictions.
This would be an in class and then homework writing assignment.