DNA computational analysis via the net

[NAME]

I am a 4th yr undergrad that has a background in Mol. Bio and Genetics and
attend a small Canadian Univ. I am currently taking a Computer Sci. course
whose premise is to utilize the net to solve an academic problem. I wish to take a nucleic acid sequence and do: homology, seq. alignment, phylogeny, and, get some insights into secondary and tertiary structure. Then make some inferences in regards to function. The faculty here are as green as I on this unfortunetly I was wondering if anyone could enlighten as to a logical step in planning a
structured approach to this does one use blast, fasta, Swiss-prot etc.
I have use of Unix machines and workstations for graphic programs like rasmol
Thanx  G.Mckenzie    GMcKenzie at Trentu.ca