Praticals In addition to the www-browser (IE), start a word editor (MS-Word or WordPad) and write down the answers to the following questions.

1. Calculate molecular weight and G+C content of the following DNA sequence trypseq. (BioEdit starts automatically) (Edit>Select All sequences --- Sequence>Nucleic Acis>Nucleotide Composition)
2. Translate into six frames. How many ORFs (Open Reading Frame) are predicted which are over 100 amino acids long Copy the longest ORF into your word editor
3. Close all BioEdit windows (except BioEdit) and create a new sequence file.(File>New Alignment --- Sequence>New sequence) Paste the longest amino acid sequence into the "New Sequence" window and give the sequence a name (e.g. test1) and select a Sequence Type (Protein). Then Apply and Close. Calculate the molecular weight of the ORF and composition. Which two amino acids are most abundant?
4. Try one or more programs predicting hydrophobic profiles. (e.g. Kyte-Doolittle) Which regions are most hydrophobic? Try different scan-window size (2, 5, 10 & 15). What do you observe?
5. Select amino 225 -245 (Click and drag). Run Helical Wheel Diagram (Sequence>Protein>Helical Wheel Diagram). Which anino acids are clustered together one one side of the helix?
6. To try to find out what protein this may be, we will use a BLAST search blast. (Accessory Application>BLAST>NCBI BLAST over the Internet). Past the amino acid sequence into the window and press Search. After a while you will se a web-page from NCBI (National Center for Biotechnology Information) with the sequences in the database that is most similar to our sequence. Which sequence is most similar to our sequence? From which organism? Has the structure been solved? If yes, how many disulfide bridges are the in the structure?
7. Close all BioEdit windows and press the following file, which starts BioEdit again. You will se several sequences. Select all sequences (Edit>Select All sequences). We will now try to align all these sequences (Accessory Application>ClustalW Multiple alignment). In the ClustalW Multiple Alignment window, clic for Full Multiple alignment, Calculate NJ tree and then press Run ClustalW. Clustalw After a while you will se a new window with the aligned sequences. There are three proteins that have a large deletion in the region around 450 to 550. Which? One sequence seems to have a deleted C-terminal. Who?
8. To see which sequence are most related, we will run the phylogenetic program PROTPARS (Protein Sequence Parsimony Method) (Accessory Application>Protpars protein parsimony method). Which sequences are SerX most related to? alignment