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CS177 week 3

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

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CS177 week 3

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

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

  4. almost finished with scavenger hunt • URL or downloading a complete list of official names for human genes (should be around 15,000 - 20,000) • retrieve a RefSeq for a human mRNA (GenBank accession should look like: NM_XXXXX) • 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)

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