QuBi/module/bio203-lab12—2020 - Revision history

imported>Lab at 19:09, 26 April 2022

2022-04-26T19:09:45Z

← Older revision		Revision as of 19:09, 26 April 2022
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	<span style="color: Seagreen;font-weight:bold;font-size:large;">Lab 10. Bioinformatics Exercises: BLAST & Genomes		<span style="color: Seagreen;font-weight:bold;font-size:large;">Lab 12. Bioinformatics Exercises: BLAST & Genomes
	==Expected Learning Outcomes==		==Expected Learning Outcomes==
	* Be able to perform NCBI BLAST search for homologous sequences in GenBank.		* Be able to perform NCBI BLAST search for homologous sequences in GenBank.
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	# The lab report is worth 50 points.		# The lab report is worth 50 points.
	# You have to complete the lab report by using the MS Word lab report template provided on Blackboard.		# You have to complete the lab report by using the MS Word lab report template provided on Blackboard.
	# Make sure to name your file with your LAST NAME-~~Lab10~~.		# Make sure to name your file with your LAST NAME-Lab12.
	# you need to EMAIL your file to your T.A. to get credit for your work.		# you need to EMAIL your file to your T.A. to get credit for your work.

imported>Lab at 02:17, 24 July 2020

2020-07-24T02:17:50Z

← Older revision		Revision as of 02:17, 24 July 2020
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	<span style="color: Seagreen;font-weight:bold;font-size:large;">Lab 12. Bioinformatics Exercises: BLAST & Genomes		<span style="color: Seagreen;font-weight:bold;font-size:large;">Lab 10. Bioinformatics Exercises: BLAST & Genomes
	==Expected Learning Outcomes==		==Expected Learning Outcomes==
	* Be able to perform NCBI BLAST search for homologous sequences in GenBank.		* Be able to perform NCBI BLAST search for homologous sequences in GenBank.
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	# The lab report is worth 50 points.		# The lab report is worth 50 points.
	# You have to complete the lab report by using the MS Word lab report template provided on Blackboard.		# You have to complete the lab report by using the MS Word lab report template provided on Blackboard.
	# Make sure to name your file with your LAST NAME-~~Lab12~~.		# Make sure to name your file with your LAST NAME-Lab10.
	# you need to EMAIL your file to your T.A. to get credit for your work.		# you need to EMAIL your file to your T.A. to get credit for your work.

imported>Lab at 20:16, 27 April 2020

2020-04-27T20:16:37Z

← Older revision		Revision as of 20:16, 27 April 2020
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	==Additional questions: answer 3 questions from the ones shown below and include in your lab report--==		==Additional questions: answer 3 questions from the ones shown below and include in your lab report--==
	# Explain the ~~following~~ BLAST ~~terms~~: “Expect” (e-value) [http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=FAQ#expect Read this FAQ]~~, “Identities”, “Gap”, “Strand”.~~		# Explain the BLAST term: “Expect” (e-value) [http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=FAQ#expect Read this FAQ]
	# Which is a statistically more significant match by BLAST, a match with an e-value=1e-5 or a match with an e-value of 1?		# Which is a statistically more significant match by BLAST, a match with an e-value=1e-5 or a match with an e-value of 1?
	# List and describe individual elements of a typical human gene based on mdm2.		# List and describe individual elements of a typical human gene based on mdm2.

imported>Lab at 19:41, 27 April 2020

2020-04-27T19:41:02Z

← Older revision		Revision as of 19:41, 27 April 2020
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	#the output is a pdf file-- save it and import into your lab report word file (as page 2) by doing an "Insert--- picture from file" in MS Word- you will have two pages: page 1 with your MDM2 sequences, and page 2 with your alignment		#the output is a pdf file-- save it and import into your lab report word file (as page 2) by doing an "Insert--- picture from file" in MS Word- you will have two pages: page 1 with your MDM2 sequences, and page 2 with your alignment

	==~~Additonal~~ questions: answer 3 questions from the ones shown below and include in your lab report--==		==Additional questions: answer 3 questions from the ones shown below and include in your lab report--==
	# Explain the following BLAST terms: “Expect” (e-value) [http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=FAQ#expect Read this FAQ], “Identities”, “Gap”, “Strand”.		# Explain the following BLAST terms: “Expect” (e-value) [http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=FAQ#expect Read this FAQ], “Identities”, “Gap”, “Strand”.
	# Which is a statistically more significant match by BLAST, a match with an e-value=1e-5 or a match with an e-value of 1?		# Which is a statistically more significant match by BLAST, a match with an e-value=1e-5 or a match with an e-value of 1?
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	#what are two determinants that can lead to the production of isoforms for a specific locus?		#what are two determinants that can lead to the production of isoforms for a specific locus?
	# What is the "GT-AG" rule? Explain how to read the sequence logos. Explain the significance of sequence conservation at exon-intron junctions.		# What is the "GT-AG" rule? Explain how to read the sequence logos. Explain the significance of sequence conservation at exon-intron junctions.
	~~# Discuss biological significance of alternative splicing, using mdm2 gene as an example.~~
	#look at your alignment from part III: what are the black boxes- the grey boxes?		#look at your alignment from part III: what are the black boxes- the grey boxes?
	#do you see many gaps/insertions?do you think there is a pattern?		#do you see many gaps/insertions?do you think there is a pattern?

	----		----

imported>Lab: /* Exercise 3. MDM2 homologs in other species */

2020-04-27T19:34:42Z

Exercise 3. MDM2 homologs in other species

← Older revision		Revision as of 19:34, 27 April 2020
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	You will need to download the human MDM2 sequence, find the mouse and fish homologs, and copy each sequence into a MS Word file using the following format:		You will need to download the human MDM2 sequence, find the mouse and fish homologs, and copy each sequence into a MS Word file using the following format:

	~~Your name (First, Last)~~
	[Blank line]		[Blank line]
	>Human MDM2		>Human MDM2

imported>Lab at 19:08, 27 April 2020

2020-04-27T19:08:47Z

← Older revision		Revision as of 19:08, 27 April 2020
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	#Now click on the "CDS" feature (coding sequence). Where does the highlighted sequence start, and in which exon? What does this point correspond to?		#Now click on the "CDS" feature (coding sequence). Where does the highlighted sequence start, and in which exon? What does this point correspond to?
	# Obtain the intron/exon gene structure and copy into your lab report file. To do this:		# Obtain the intron/exon gene structure and copy into your lab report file. To do this:
	##~~go back to~~ the Genbank page for AF527840 ~~(as instructed above)~~		##on top of the Genbank page for AF527840 click on the "Graphics" link
	##click on the "Graphics" link
	##you will see a window with a diagram, showing the genomic sequence in green, the primary transcript in purple, and the coding sequence in red		##you will see a window with a diagram, showing the genomic sequence in green, the primary transcript in purple, and the coding sequence in red
	##copy and paste this diagram into your lab report (or create a desktop picture, crop as needed and paste into your lab report file)		##copy and paste this diagram into your lab report (or create a desktop picture, crop as needed and paste into your lab report file)

imported>Lab: /* Exercise 2. Explore the structure of human mdm2 gene */

2020-04-27T19:04:49Z

Exercise 2. Explore the structure of human mdm2 gene

← Older revision		Revision as of 19:04, 27 April 2020
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	#Go back to the GenBank file and click on the "mRNA" feature, on the left of the window. The exons will be highlighted on the sequence. Scroll back up to the beginning of the gene.		#Go back to the GenBank file and click on the "mRNA" feature, on the left of the window. The exons will be highlighted on the sequence. Scroll back up to the beginning of the gene.
	#Write down the coordinates (1st and last nucleotide) for exon 1 and for exon 2 (hint: you do not need to count the bases).		#Write down the coordinates (1st and last nucleotide) for exon 1 and for exon 2 (hint: you do not need to count the bases).
	#Now click on the "CDS" feature (coding sequence). Where does the highlighted sequence start, and in which exon?		#Now click on the "CDS" feature (coding sequence). Where does the highlighted sequence start, and in which exon? What does this point correspond to?
	# Obtain the intron/exon gene structure and copy into your lab report file. To do this:		# Obtain the intron/exon gene structure and copy into your lab report file. To do this:
	##go back to the Genbank page for AF527840 (as instructed above)		##go back to the Genbank page for AF527840 (as instructed above)

imported>Lab at 18:57, 27 April 2020

2020-04-27T18:57:47Z

← Older revision		Revision as of 18:57, 27 April 2020
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	#Click on "Gene", located on the right side of the page, under "Related Information"		#Click on "Gene", located on the right side of the page, under "Related Information"
	#Write down the gene name, and a brief description of its function		#Write down the gene name, and a brief description of its function
	#Scroll down the page: you will se a window showing the various transcripts encoded by this gene		#Scroll down the page: you will se a window showing the various transcripts encoded by this gene. The vertical bars are the exonic sequences, and the coding portions are indicated in dark green.
	#find transcript variant 1-isoform a: this is the longest isoform. How many exons and introns does this transcript have? How many nucleotides does the coding sequence contain? How many amino acids does it code for?		#find transcript variant 1-isoform a: this is the longest isoform. How many exons and introns does this transcript have? How many nucleotides does the coding sequence contain? How many amino acids does it code for?
	#Go back to the GenBank file and click on the "mRNA" feature, on the left of the window. The exons will be highlighted on the sequence. Scroll back up to the beginning of the gene.		#Go back to the GenBank file and click on the "mRNA" feature, on the left of the window. The exons will be highlighted on the sequence. Scroll back up to the beginning of the gene.

imported>Lab at 18:45, 27 April 2020

2020-04-27T18:45:36Z

imported>Lab at 18:11, 27 April 2020

2020-04-27T18:11:13Z

← Older revision		Revision as of 18:11, 27 April 2020
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	#Scroll down the page: you will se a window showing the various transcripts encoded by this gene		#Scroll down the page: you will se a window showing the various transcripts encoded by this gene
	#find transcript variant 1-isoform a: this is the longest isoform. How many exons and introns does this transcript have? How many nucleotides is the coding sequence? How many amino acids does it code for?		#find transcript variant 1-isoform a: this is the longest isoform. How many exons and introns does this transcript have? How many nucleotides is the coding sequence? How many amino acids does it code for?
	#~~Read~~ the GenBank file and ~~find out from~~ the feature ~~table how many introns and~~ exons ~~this~~ sequence ~~has according~~ to the ~~"mRNA"~~ and ~~"CDS" features~~.		#Go back to the GenBank file and click on the "mRNA" feature, on the left of the window. The exons will be highlighted on the sequence. Scroll back up to the beginning of the gene.
			#Write down the coordinates (1st and last nucleotide) for exon 1 and for exon 2.
			#Now click on the "CDS" features (coding sequence. Where does the highlighted sequence start, and in which exon?

	# ~~Click~~ on "~~mRNA~~" and ~~notice that~~ exon ~~sequences are now highlighted~~
	# Obtain the intron/exon gene structure and copy into your lab report file. To do this:		# Obtain the intron/exon gene structure and copy into your lab report file. To do this:
	##go back to the Genbank page for AF527840 (as instructed above)		##go back to the Genbank page for AF527840 (as instructed above)
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	##copy and paste this diagram into your lab report (or create a desktop picture, crop as needed and paste into your lab report file)		##copy and paste this diagram into your lab report (or create a desktop picture, crop as needed and paste into your lab report file)
	# Answer the following questions, in your lab report file:		# Answer the following questions, in your lab report file:
	## ~~What is the total length of exons, introns, and coding sequences of this gene?~~		## Do all exon sequences code for proteins? Which exons are non-coding in mdm2?
	~~## Are~~ all exon sequences code for proteins? Which exons are non-coding in mdm2?		## Copy/past and align the first 5 bases of all introns. Which bases are conserved near intron start ("donor site")?
	## ~~Align~~ the first 5 bases of all introns. Which bases are conserved near intron start ("donor site")?		## Do the same with the last 5 bases of all introns. Which bases are conserved near intron end ("acceptor site")?
	## ~~Align~~ the last 5 bases of all introns. Which bases are conserved near intron end ("acceptor site")?
	## Using [http://weblogo.berkeley.edu/ WebLogo] and make a sequence logo for the acceptor site and another sequence logo for the donor site. To do so, copy & paste individual sequences at the acceptor site into [http://weblogo.threeplusone.com/create.cgi this text box] and click "Create Logo". Save the resulting image file and paste it into your lab report file. Repeat for the donor-site sequences.		## Using [http://weblogo.berkeley.edu/ WebLogo] and make a sequence logo for the acceptor site and another sequence logo for the donor site. To do so, copy & paste individual sequences at the acceptor site into [http://weblogo.threeplusone.com/create.cgi this text box] and click "Create Logo". Save the resulting image file and paste it into your lab report file. Repeat for the donor-site sequences.
	<center>		<center>
	~~Table 1. ''mdm2'' Exons~~
	~~{\| class="wikitable"~~
	\|-
	~~! Exon # !! Start Position !! End Position !! Length~~
	\|-
	~~\| #1 \|\| 1971 \|\| 2271 \|\| 301~~
	\|-
	~~\| #2 \|\| ? \|\| ? \|\| ?~~
	\|}

	~~Table 2. ''mdm2'' Introns~~
	~~{\| class="wikitable"~~
	\|-
	! Intro Number !! Start Position !! End Position !! Length !! First 5 bases !! Last 5 bases !! Phase*
	\|-
	~~\| #1 \|\| 2272 \|\| 2987 \|\| 616 \|\| GTACT \|\| TGTAG \|\| ?~~
	\|-
	~~\| #2 \|\| ? \|\| ? \|\| ? \|\| ? \|\| ? \|\| ?~~
	\|}

	* Introns have phases. Phase 0 introns sit between 2 codons, phase 1 intron sit between the 1st codon position and the 2nd codon position, and phase 3 introns sit between the 2nd and 3rd codon position. How would you find out the phase of an intron? [Hint, use Table 3 CDS positions below].

	~~Table 3. ''mdm2'' Coding Sequences (CDS)~~
	~~{\| class="wikitable"~~
	\|-
	~~! CDS # !! Start Position !! End Position !! Length~~
	\|-
	~~\| #1 \|\| 2992 \|\| 3072 \|\| 81~~
	\|-
	~~\| #2 \|\| ? \|\| ? \|\| ?~~
	\|}
	</center>		</center>
	----		----

← Older revision		Revision as of 18:45, 27 April 2020
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	# Search [http://www.ncbi.nlm.nih.gov/sites/entrez?db=Nucleotide GenBank] using the accession AF527840.		# Search [http://www.ncbi.nlm.nih.gov/sites/entrez?db=Nucleotide GenBank] using the accession AF527840.
	#Click on "Gene", located on the right side of the page, under "Related Information"		#Click on "Gene", located on the right side of the page, under "Related Information"
	#Write down the gene name, a a brief description of its function		#Write down the gene name, and a brief description of its function
	#Scroll down the page: you will se a window showing the various transcripts encoded by this gene		#Scroll down the page: you will se a window showing the various transcripts encoded by this gene
	#find transcript variant 1-isoform a: this is the longest isoform. How many exons and introns does this transcript have? How many nucleotides is the coding sequence? How many amino acids does it code for?		#find transcript variant 1-isoform a: this is the longest isoform. How many exons and introns does this transcript have? How many nucleotides does the coding sequence contain? How many amino acids does it code for?
	#Go back to the GenBank file and click on the "mRNA" feature, on the left of the window. The exons will be highlighted on the sequence. Scroll back up to the beginning of the gene.		#Go back to the GenBank file and click on the "mRNA" feature, on the left of the window. The exons will be highlighted on the sequence. Scroll back up to the beginning of the gene.
	#Write down the coordinates (1st and last nucleotide) for exon 1 and for exon 2.		#Write down the coordinates (1st and last nucleotide) for exon 1 and for exon 2 (hint: you do not need to count the bases).
	#Now click on the "CDS" ~~features~~ (coding sequence. Where does the highlighted sequence start, and in which exon?		#Now click on the "CDS" feature (coding sequence). Where does the highlighted sequence start, and in which exon?
	# Obtain the intron/exon gene structure and copy into your lab report file. To do this:		# Obtain the intron/exon gene structure and copy into your lab report file. To do this:
	##go back to the Genbank page for AF527840 (as instructed above)		##go back to the Genbank page for AF527840 (as instructed above)
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	##copy and paste this diagram into your lab report (or create a desktop picture, crop as needed and paste into your lab report file)		##copy and paste this diagram into your lab report (or create a desktop picture, crop as needed and paste into your lab report file)
	# Answer the following questions, in your lab report file:		# Answer the following questions, in your lab report file:
	## Do all exon sequences code for proteins? ~~Which exons are~~ non-coding in mdm2?		## Do all exon sequences code for proteins? Are there non-coding exons in mdm2, and if so which ones?
	## Copy/past and align the first 5 bases of all introns. Which bases are conserved near intron start ("donor site")?		## Copy/past and align the first 5 bases of all introns. Which bases are conserved near intron start ("donor site")?
	## Do the same with the last 5 bases of all introns. Which bases are conserved near intron end ("acceptor site")?		## Do the same with the last 5 bases of all introns. Which bases are conserved near intron end ("acceptor site")?