CS177 week 3

1
CS177 week 3

• scavenger hunt
• team mini-project
• start in class
• finish as part of homework
• this will include a mixture of things we have and
  have not covered in class
• short answers - lower grades for long answers
• give references documenting where you got it from
• ok to copy and paste, but you need to actually
  know what it says, and you need to indicate if it
  is your words or copy and paste
• due next Monday
• submit electronic document to TA (one per team)
• this will be graded

2
items in scavenger hunt

1. statement of difference between transcription and
   translation
2. two different ways of tabulating the genetic code
3. one database that specializes in proteins
4. two places where you can get 3D structures of
   proteins
5. URL that has a tutorial in perl programming
6. two URLs for web servers that perform multiple
   alignment of DNA or RNA sequences

3
more items in scavenger hunt

1. database of post-translational modifications
2. reference to the earliest gene expression
   microarray study you can find
3. references to two microarray studies that examine
   human diseases
4. a database that groups genes in different species
   by similarity in DNA or RNA sequence
5. explanation of the Bonferroni correction
6. URL of a web server that predicts protein
   secondary structure using a hidden markov model

4
almost finished with scavenger hunt

1. URL or downloading a complete list of official
   names for human genes (should be around 15,000 -
   20,000)
2. retrieve a RefSeq for a human mRNA (GenBank
   accession should look like NM_XXXXX)
3. find or write a perl script that takes the
   sequence in 13 and chops off everything to the
   left of the first codon for methionine AND chops
   off everything to the right of the first stop
   codon that follows that methionine (hint the
   methionine and the stop codon need to be in the
   same reading frame)