QLanners Week 2 - Revision history

Qlanners: added line break in acknowledgements

2017-09-12T06:44:06Z

added line break in acknowledgements

Qlanners: edited link to hw partner's page

2017-09-12T06:40:48Z

edited link to hw partner's page

Qlanners: fixed the signature in acknowledgements

2017-09-12T05:09:50Z

fixed the signature in acknowledgements

Qlanners: added a final acknowledgement and bullet points to this section

2017-09-12T05:08:53Z

added a final acknowledgement and bullet points to this section

Qlanners: fixed top header

2017-09-12T04:25:39Z

fixed top header

Qlanners: added acknowledgements and small line break formats

2017-09-12T04:25:14Z

added acknowledgements and small line break formats

Qlanners: added more information to the electronic journal, and also included my references

2017-09-09T07:12:35Z

added more information to the electronic journal, and also included my references

Qlanners: added to electronic journal with parts of the steps taken

2017-09-09T06:45:52Z

added to electronic journal with parts of the steps taken

Qlanners: added first part of the journal including all of code used to solve assignment

2017-09-09T05:51:11Z

added first part of the journal including all of code used to solve assignment

Qlanners: added links using template

2017-09-09T03:13:40Z

added links using template

@@ Line 39: / Line 39: @@
 *I texted my homework partner [https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/User:Nicolekalcic Nicole Kalcic] on two occasions over the weekend to ensure that we were both on track and to review each others' pages and answer questions we had regarding the assignment. <br>
 * I referenced the website https://stackoverflow.com/questions/931092/reverse-a-string-in-python for how to best reverse the order of a string in python.
-*While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source. [[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 22:09, 11 September 2017 (PDT)
+*While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source. <br>
 ==References==

@@ Line 37: / Line 37: @@
 ==Acknowledgements==
-*I texted my homework partner [[https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/User:Nicolekalcic Nicole Kalcic]] on two occasions over the weekend to ensure that we were both on track and to review each others' pages and answer questions we had regarding the assignment. <br>
+*I texted my homework partner [https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/User:Nicolekalcic Nicole Kalcic] on two occasions over the weekend to ensure that we were both on track and to review each others' pages and answer questions we had regarding the assignment. <br>
 * I referenced the website https://stackoverflow.com/questions/931092/reverse-a-string-in-python for how to best reverse the order of a string in python.
 *While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source. [[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 22:09, 11 September 2017 (PDT)

@@ Line 39: / Line 39: @@
 *I texted my homework partner [[https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/User:Nicolekalcic Nicole Kalcic]] on two occasions over the weekend to ensure that we were both on track and to review each others' pages and answer questions we had regarding the assignment. <br>
 * I referenced the website https://stackoverflow.com/questions/931092/reverse-a-string-in-python for how to best reverse the order of a string in python.
-*While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source. [[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]])
+*While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source. [[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 22:09, 11 September 2017 (PDT)
 ==References==

@@ Line 37: / Line 37: @@
 ==Acknowledgements==
-I texted my homework partner [[https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/User:Nicolekalcic Nicole Kalcic]] on two occasions over the weekend to ensure that we were both on track and to review each others' pages and answer questions we had regarding the assignment. <br>
+*I texted my homework partner [[https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/User:Nicolekalcic Nicole Kalcic]] on two occasions over the weekend to ensure that we were both on track and to review each others' pages and answer questions we had regarding the assignment. <br>
-While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source. [[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]])
+* I referenced the website https://stackoverflow.com/questions/931092/reverse-a-string-in-python for how to best reverse the order of a string in python.
 ==References==

← Older revision		Revision as of 04:25, 12 September 2017
Line 1:		Line 1:
−	==The Genetic Code Assignment==	+	=The Genetic Code Assignment=

@@ Line 1: / Line 1: @@
 ==The Genetic Code Assignment==
+==Laboratory Notebook and Answers==
 I used a combination of my knowledge of DNA transcription and translation from my previous biology classes, along with a little bit of code to do this assignment.
@@ Line 31: / Line 29: @@
 The results were as follows:
   -1   Nothing (Full outputted protein sequence from function: N-_NAASGTGGWVIRGTWY_HT-C)
--2   N-KMPPAELAAGLYAEHGISI-C
+ -2   N-KMPPAELAAGLYAEHGISI-C
--3   N-KCRQRNWRLGYTRNMVLAY-C
+ -3   N-KCRQRNWRLGYTRNMVLAY-C
 Finally, to answer the question at the end of the assignment, reading frames +1, -2, and -3 were all open reading frames.
@@ Line 39: / Line 37: @@
 ==Acknowledgements==
 ==References==
-LMU BioDB 2017. (2017). Week 2. Retrieved September 8, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_2
+LMU BioDB 2017. (2017). Week 2. Retrieved September 8, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_2 <br>
 Swanson, K. E. (2013). Translation DNA to Protein [Forum post]. Retrieved September 8, 2017, from https://stackoverflow.com/questions/19521905/translation-dna-to-protein

@@ Line 11: / Line 11: @@
 ’-cgtatgctaataccatgttccgcgtataacccagccgccagttccgctggcggcatttta-3’
-The most efficient way I thought of doing this assignment was making a class called DNA that had functions within the class to find the DNA strand's complementary strands and protein sequences from the various reading frames.
+The most efficient way I thought of doing this assignment was making a class called DNA that had functions within the class to find the DNA strand's complementary strands and protein sequences from the various reading frames. This class had one provided attribute, which was the sequence of the DNA. I started off by making the variable "templateDNA" of the class "DNA" and "sequence" attribute of the sequence above.
-The first step was to create a function that I called compStrand to take the input template strand and output the complementary strand. In order to make the code easier, I just took off the 5' and 3' of the string. And then after passing the template DNA strand through the function, I was sure to add the end labels back on, being sure to put them on in the reverse 3' to 5' order.
+The first step was to create a function that I called "compStrand" to take the input template strand and output the complementary strand. In order to make the code easier, I just took off the 5' and 3' of the string. And then after passing the template DNA strand through the function, I was sure to add the end labels back on, being sure to put them on in the reverse 3' to 5' order. As for the code, the function just iterated through the input string and replaced each letter with its corresponding base (a to t and g to c).
-The complementary strand was found to be:
+After calling this function on the "templateDNA", the complementary strand was found to be:
 '-gcatacgattatggtacaaggcgcatattgggtcggcggtcaaggcgaccgccgtaaaat-5'
-As for the reading frames portion of this assignment, I created another function, called protein, within the class. This function took one argument which was the location of the start of the reading frame.
+As for the reading frames portion of this assignment, I created another function, called protein, within the class. This function took one argument which was the location of the start of the reading frame. The function shifted the string the appropriate number of spaces to start at that provided location. The function then broke the string into strings of 3 characters and appended each string of three letters to a list called "codons". This list was then iterated through and matched to a value in the dictionary "codontable", which was used from an online source (Swanson, 2013), which had the correct corresponding amino acid letter for each three letter codon code. These amino acid letters were then strung together in a final string called "protein" and printed.
 For reading frames +1,+2, and +3, I was able to just use the template DNA strand that was already provided, as this string was oriented in the 5' to 3' direction.
-Hence I called the function protein() on this strand using the arguments 1, 2 and 3. A _ in the outputted protein sequence indicated a stop codon, so this was also taken into account, as any codons beyond that point would not be translated. I included the full output from the function called as well in parentheses after the shortened protein sequence. I then added the N and C terminus endings to either end of these output strings.
+Hence I called the function "protein()" on this strand using the arguments 1, 2 and 3. A "_" in the outputted protein sequence indicated a stop codon, so this was also taken into account, as any codons beyond that point would not be translated. I included the full output from the function called as well in parentheses after the shortened protein sequence. I then added the N and C terminus endings to either end of these output strings.
 The results were as follows:
   +1   N-RMLIPCSAYNPAASSAGGIL-C
@@ Line 28: / Line 28: @@
   +3  N-YANTMFRV-C    (Full outputted protein sequence from function: N-YANTMFRV_PSRQFRWRHF-C)
-As for the -1, -2, and -3 reading frames, I had to assign the complementary strand computed above to a new variable (called compStrand) and then I used the function compStrand[::
+As for the -1, -2, and -3 reading frames, I had to assign the complementary strand computed above to a new variable (called "compStrand") and then I used the function "compStrand[::-1]" to reverse the order of the complementary strand to the 5' to 3' direction. I then assigned this string as the "sequence" property to a new variable "bottomStrand" of the class "DNA". From here, I called the function protein with arguments 1,2 and 3 as I did above to find the -1, -2 and -3 reading frames from the bottom strand in the 5' to 3' direction.
-  +3
+The results were as follows:
 ==Acknowledgements==
 ==References==
 ==Links==
 {{Template:Links|2}}

@@ Line 8: / Line 8: @@
 I used a combination of my knowledge of DNA transcription and translation from my previous biology classes, along with a little bit of code to do this assignment.
-The most efficient way I thought of doing this assignment was making a class called DNA that functions within the class to find the DNA strand's complementary strands and protein sequences from the various reading frames.
+The original template strand provided was:
-The code for this class is as follows:
+The most efficient way I thought of doing this assignment was making a class called DNA that had functions within the class to find the DNA strand's complementary strands and protein sequences from the various reading frames.
-	def __init__(self, sequence):
+The first step was to create a function that I called compStrand to take the input template strand and output the complementary strand. In order to make the code easier, I just took off the 5' and 3' of the string. And then after passing the template DNA strand through the function, I was sure to add the end labels back on, being sure to put them on in the reverse 3' to 5' order.
-	def compStrand(self):
+The complementary strand was found to be:
-		newDNA = ''
+As for the reading frames portion of this assignment, I created another function, called protein, within the class. This function took one argument which was the location of the start of the reading frame.
+For reading frames +1,+2, and +3, I was able to just use the template DNA strand that was already provided, as this string was oriented in the 5' to 3' direction.
-	def RNA(self):
+Hence I called the function protein() on this strand using the arguments 1, 2 and 3. A _ in the outputted protein sequence indicated a stop codon, so this was also taken into account, as any codons beyond that point would not be translated. I included the full output from the function called as well in parentheses after the shortened protein sequence. I then added the N and C terminus endings to either end of these output strings.
-		newDNA = ''
+The results were as follows:
-		for i in self.sequence:
+ +1   N-RMLIPCSAYNPAASSAGGIL-C
-			if i == 't':
+ +2  N-VC-C   (Full outputted protein sequence from function: N-VC_YHVPRITQPPVPLAAF-C)
-				newDNA += 'u'
+ +3  N-YANTMFRV-C    (Full outputted protein sequence from function: N-YANTMFRV_PSRQFRWRHF-C)
 ==Acknowledgements==

← Older revision		Revision as of 05:51, 9 September 2017
Line 6:		Line 6:
	==Laboratory Notebook==		==Laboratory Notebook==

		+	I used a combination of my knowledge of DNA transcription and translation from my previous biology classes, along with a little bit of code to do this assignment.
		+
		+	The most efficient way I thought of doing this assignment was making a class called DNA that functions within the class to find the DNA strand's complementary strands and protein sequences from the various reading frames.
		+
		+	The code for this class is as follows:
		+	{{border\|
		+	class DNA:
		+
		+	def __init__(self, sequence):
		+	self.sequence = sequence
		+
		+	def compStrand(self):
		+
		+	newDNA = ''
		+	for i in self.sequence:
		+	if i == 'a':
		+	newDNA += 't'
		+	elif i == 't':
		+	newDNA += 'a'
		+	elif i == 'g':
		+	newDNA += 'c'
		+	elif i == 'c':
		+	newDNA += 'g'
		+	print(newDNA)
		+	return newDNA
		+
		+
		+
		+	def RNA(self):
		+	newDNA = ''
		+	for i in self.sequence:
		+	if i == 't':
		+	newDNA += 'u'
		+	else:
		+	newDNA += i
		+
		+	print(newDNA)
		+
		+	def protein(self, start):
		+	seqCap = self.sequence.upper()
		+	codons = list()
		+	codontable = {
		+	'ATA':'I', 'ATC':'I', 'ATT':'I', 'ATG':'M',
		+	'ACA':'T', 'ACC':'T', 'ACG':'T', 'ACT':'T',
		+	'AAC':'N', 'AAT':'N', 'AAA':'K', 'AAG':'K',
		+	'AGC':'S', 'AGT':'S', 'AGA':'R', 'AGG':'R',
		+	'CTA':'L', 'CTC':'L', 'CTG':'L', 'CTT':'L',
		+	'CCA':'P', 'CCC':'P', 'CCG':'P', 'CCT':'P',
		+	'CAC':'H', 'CAT':'H', 'CAA':'Q', 'CAG':'Q',
		+	'CGA':'R', 'CGC':'R', 'CGG':'R', 'CGT':'R',
		+	'GTA':'V', 'GTC':'V', 'GTG':'V', 'GTT':'V',
		+	'GCA':'A', 'GCC':'A', 'GCG':'A', 'GCT':'A',
		+	'GAC':'D', 'GAT':'D', 'GAA':'E', 'GAG':'E',
		+	'GGA':'G', 'GGC':'G', 'GGG':'G', 'GGT':'G',
		+	'TCA':'S', 'TCC':'S', 'TCG':'S', 'TCT':'S',
		+	'TTC':'F', 'TTT':'F', 'TTA':'L', 'TTG':'L',
		+	'TAC':'Y', 'TAT':'Y', 'TAA':'_', 'TAG':'_',
		+	'TGC':'C', 'TGT':'C', 'TGA':'_', 'TGG':'W',
		+	}
		+
		+	seqcut = seqCap[start:]
		+	while len(seqcut) >= 3:
		+	codons.append(seqcut[:3])
		+	seqcut = seqcut[3:]
		+	print(codons)
		+
		+	protein = ''
		+	for codes in codons:
		+	protein += codontable[codes]
		+	print(protein)}}

	==Acknowledgements==		==Acknowledgements==

← Older revision		Revision as of 03:13, 9 September 2017
Line 11:		Line 11:

	==References==		==References==
		+
		+
		+	==Links==
		+	{{Template:Links\|2}}