Nanguiano Week 4

Transcription and Translation “Taken to the Next Level”

First, I needed to log in to my LMU CS account to access the data used in this weeks assignment.

ssh nanguia1@lion.lmu.edu

Next, I needed to enter the folder that I'd created for the class, and create a new folder for this week's assignment.

cd biodb
mkdir week4

Next, I moved into Dondi's directory so I could obtain the file required for the assignment - infA-E.coli-K12.txt.

cd ~dondi/xmlpipedb/data
cp infA-E.coli-K12.txt ~nanguia1/biodb/week4

Then, I moved into my directory to prepare to do the assignment.

cd ~nanguia1/biodb/week4

For each of the following questions pertaining to this gene, provide (a) the actual answer, and (b) the sequence of text-processing commands that calculates this answer. Specific information about how these sequences can be identified is included after the list of questions.

Modify the gene sequence string so that it highlights or “tags” the special sequences within this gene, as follows (ellipses indicate bases in the sequence; note the spaces before the start tag and after the end tag):
- -35 box of the promoter
```
... <minus35box>...</minus35box> ...
```
- -10 box of the promoter
```
... <minus10box>...</minus10box> ...
```
- transcription start site
```
... <tss>...</tss> ...
```
- ribosome binding site
```
... <rbs>...</rbs> ...
```
- start codon
```
... <start_codon>...</start_codon> ...
```
- stop codon
```
... <stop_codon>...</stop_codon> ...
```
- terminator
```
... <terminator>...</terminator> ...
```
What is the exact mRNA sequence that is transcribed from this gene?
What is the amino acid sequence that is translated from this mRNA?

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Nicole Anguiano
BIOL 367, Fall 2015

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Nanguiano Week 4

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Transcription and Translation “Taken to the Next Level”

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