HW 05 30.10 Time Warp, bio

1. Calculate dynamic time warp distance(s) (and show alignments) between time series
S= 2 3 5 7 8 8 6 2 5 2 3 4 7 5
T= 4 7 7 8 2 2 6 5 3 4 5 5 6

2. Study some alternative definitions of time warp recurrence. Explain what are the effects of those alternatives. Illustrate.

3. Where would you foresee & propose time warp to be used - attempt to find something relevant to you. It would be nice if you could identify and describe respective data.

4. Use the two protein sequences X and Y (in Fasta format). Draw the dot-plot (e.g. using some web based tool). Attempt to vary some parameters. Describe the sequences.

>GeneX
maghlasdfafspppgggdgpggpepgwvdpprtwlsfqgppggpgigpgvgpgsevwgi
ppcglvpqgglepppyefcggmaycgpqvgvtsqpegeagvgvesnsdgaspepctvtpg
avklekekleqnpeesqdikalqkeleqfakllkqkritlgytqadigltlgvlfgkvfs
qtticrfealnmcklrpqlsfkllqkwveeadnnenlqeickaetlvqarkrkrtsienr
vrgnlenlflqcpkptlqqishiaqqlglekdvlcpkptlqqishiaqqlglekdvlrlwf
cnrrqkgkrsssdyaqredfeaagspfsggpvsfplapgphfgtpgygsphftalyss
vpfpegeafppvsvttlgspmhsn
>GeneY
maghlpvsfplapgphfgtpgygsphftprtwlsfqgppggpgigpgvgpgsevwgi
maghlasdfafspppgggdgpggpepgwvdpprtwlsfqgppggpgigpgvgpgsevwgi
ppcpppyefcggmaycgpqvgvglvpqggletsqpegeagvgvesnsdgaspepctvtp
avklekekleqnpeesqdikalqkeleqfakllkqkritlgytqadvgltlgvlfgkvfs
qtticrfealqlsfknmcklrpllqkwvcpkptlqqishiaqqlglekdvlcpkptlqqi
fcggmaycgpqvgvtsqpegeagvgvesnsdgaspepctvtpg
shiaqqlglekdvleeadnnenlqeickaetlvqarkrkrtsienr
vrgnlenlflqcpkptlqqishiaqqlglekdvvrvwfcnrrqkgkrsssdyaqredfea
agspfsggpvsfplapgphfgtpgygsphftalyssvpfpegeafppvsvttlgspmhsn

5. Study the BLAST database search tool (eg. from tutorials, EBI, NCBI websites, ...). Describe what are the parameters that BLAST uses and what is the basic output. Estimate the speed of BLAST using some large public database search (how many sequences in the database, how fast does the query run).

6. Bonus (3p) Provide a strategy to automatically develop generalised edit operations and costs for some application scenario. Write a report of max 3 pages.