Biol425 2013 - Revision history

imported>Weigang: /* March 27 (No Class) */

2014-03-08T19:54:09Z

March 27 (No Class)

← Older revision		Revision as of 19:54, 8 March 2014
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	===March 27 (No Class)===		===March 27 (No Class)===
	'''~~Spring Break~~'''		'''See assignments above'''
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imported>Weigang: /* May 22: Final Project Due */

2013-05-20T19:12:51Z

May 22: Final Project Due

← Older revision		Revision as of 19:12, 20 May 2013
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	----		----

	===May 22: Final Project Due===		===May 22: Final Project Due (<font color="red">5pm in my office @HN839</font>)===
	* Sample Projects		* Sample Projects
	# <font color="blue">[Claimed]</font>(Genomics) Explore codon usage I: Write a PERL script to parse the [http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=224326 codon usage table of Borrelia burgdorferi B31]. Test if the synonymous codons are equally used or there are statistically significant biases.		# <font color="blue">[Claimed]</font>(Genomics) Explore codon usage I: Write a PERL script to parse the [http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=224326 codon usage table of Borrelia burgdorferi B31]. Test if the synonymous codons are equally used or there are statistically significant biases.

imported>Weigang: /* May 8: Final Project (Session I) */

2013-05-08T22:50:51Z

May 8: Final Project (Session I)

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 | (1) extract ancestral sequences in the proml outfile; (2) identify changes on each tree branch
 | Test of significance of reconstructed sequences
 |}

imported>Weigang: /* May 8: Final Project (Session I) */

2013-05-08T21:17:39Z

May 8: Final Project (Session I)

← Older revision		Revision as of 21:17, 8 May 2013
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	\|-		\|-
	\| CpG depletion in human genome		\| CpG depletion in human genome
	\| ~~microarray, transcriptome,~~ gene ~~expression, fold change~~		\| role of CpG islands in gene regulation
	\| ~~CCLE expression matrix~~ of ~~breast~~-~~cancer cells~~		\| GBB.1con; a partial Human genome sequence
	\| (1) ~~a heat map~~; (2) ~~classify into subtypes and use cutree to separate into two groups; (3) A list~~ of ~~genes ordered by their~~ significance ~~in expression profile between the two subtypes~~		\| dinucleotide frequencies
	~~\| Pathway analysis~~ of ~~significantly expressed genes~~		\| test significance of over and under-representation of CpG

			\|-
			\| Ancestral sequence changes
			\| phylogenetic reconstruction; phylogenetic inference
			\| OspAB.fas
			\| (1) extract ancestral sequences in the proml outfile; (2) identify changes on each tree branch
			\| Test of significance of reconstructed sequences

	\|}		\|}

imported>Weigang: /* May 8: Final Project (Session I) */

2013-05-08T20:19:43Z

May 8: Final Project (Session I)

← Older revision		Revision as of 20:19, 8 May 2013
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	\| What sites are under positive natural selection, based on MEME-Hyphy analysis?		\| What sites are under positive natural selection, based on MEME-Hyphy analysis?
	\| Build a LWP-based pipeline for automated analysis using DataMonkey		\| Build a LWP-based pipeline for automated analysis using DataMonkey


	\|-		\|-
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	\| BLAST, alignment, phylogeny		\| BLAST, alignment, phylogeny
	\| OspA sequence & Four Genome protein database		\| OspA sequence & Four Genome protein database
	\| A phylogenetic tree in PDF		\| (1) "fetch-seq.pl" to extract FASTA sequences of BLAST hits. (2) A phylogenetic tree in PDF
	\| How to root a phylogenetic tree? How to test the statistical significance of a tree?		\| How to root a phylogenetic tree? How to test the statistical significance of a tree?

			\|-
			\| Transcriptomes of cancer subtypes I
			\| microarray, transcriptome, gene expression, fold change
			\| leukemiasEset dataset
			\| (1) a heat map after gene filtering; (2) A list of genes ordered by their significance in expression profile between the four subtypes, using rowftest().
			\| Pathway analysis of significantly expression

			\|-
			\| Transcriptomes of cancer subtypes II
			\| microarray, transcriptome, gene expression, fold change
			\| CCLE expression matrix of breast-cancer cells
			\| (1) a heat map; (2) classify into subtypes and use cutree to separate into two groups; (3) A list of genes ordered by their significance in expression profile between the two subtypes
			\| Pathway analysis of significantly expressed genes

	\|-		\|-
	\| ~~Transcriptomes of Two Cancers~~		\| CpG depletion in human genome
	\| microarray, transcriptome, gene expression, fold change		\| microarray, transcriptome, gene expression, fold change
	\| CCLE ~~matrices~~ of two groups ~~of cancers~~		\| CCLE expression matrix of breast-cancer cells
	\| A list of genes ordered by their significance in expression profile between the two ~~cancer types; a heat map~~		\| (1) a heat map; (2) classify into subtypes and use cutree to separate into two groups; (3) A list of genes ordered by their significance in expression profile between the two subtypes
	\| Pathway analysis of significantly expressed genes		\| Pathway analysis of significantly expressed genes

	\|}		\|}
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imported>Weigang: /* May 8: Final Project (Session I) */

2013-05-08T20:07:47Z

May 8: Final Project (Session I)

← Older revision		Revision as of 20:07, 8 May 2013
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	! Statistical analysis		! Statistical analysis
	\|-		\|-
	\| Codon Usage		\| Codon Usage I
	\| genetic code, codon degeneracy, codon usage, GC%		\| genetic code, codon degeneracy, codon usage, GC%
	\| CUTG table		\| CUTG table
	\| Frequencies of codons, grouped by amino acid; GC%		\| Frequencies of codons, grouped by amino acid; GC%
	\| Are synonymous codons uniformly used? What are the possible factors causing biased codon usages?		\| Are synonymous codons uniformly used? (Hint: use chisq.test in R.
			\|-
			\| Codon Usage II
			\| genetic code, codon degeneracy, codon usage, GC%
			\| GBB.seq, which is a FASTA file of n=1738 ORF sequences of B. burgdorferi B31. Use Bio::SeqIO to read the file and Bio::Tools::CodonUsage to translate codons
			\| Frequencies of codons, grouped by amino acid; GC%
			\| What are the possible factors causing biased codon usages? Compare the codon usage of virulence-related genes with others. Do you expect the usage more or less biased?
	\|-		\|-
	\| Splicing Signal		\| Splicing Signal
	\| intron, exon, splicing, donor site, acceptor site, information		\| intron, exon, splicing, donor site, acceptor site, information
	\| ~~10 intron-exon junction sequences~~		\| mdm2 gene sequence and a coordinate file of introns
	\| ~~Information~~ content (in bits) at each site		\| (1) Extract donor and acceptor sequences, (2) Calculate information content (in bits) at each site
	\| ~~Understand~~ sequence ~~logo~~		\| Plot a WebLogo

			\|-
			\| Protein sequence evolution
			\| homology, orthology, paralogy, neufunctionalization of duplicated genes, homology modeling
			\| A FASTA file of OspA and OspB sequences from 8 Borrelia species; OspA structure from PDB
			\| (1) alignment, (2) midpoint-rooted phylogeny, (3) a homology model of OspB.
			\| What sites vary between species? What between OspA and OspB? Where are these sites located on the OspA structure?

			\|-
			\| DataMonkey pipeline
			\| Positive natural selection
			\| A FASTA file of ospB coding sequences from 8 Borrelia species
			\| What sites are under positive natural selection, based on MEME-Hyphy analysis?
			\| Build a LWP-based pipeline for automated analysis using DataMonkey


	\|-		\|-
	\| Phylogenetics Pipeline		\| Phylogenetics Pipeline

imported>Weigang: /* May 8: Final Project (Session I) */

2013-05-05T17:58:50Z

May 8: Final Project (Session I)

← Older revision		Revision as of 17:58, 5 May 2013
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	! Statistical analysis		! Statistical analysis
	\|-		\|-
	\| ~~Borrelia~~ Codon Usage		\| Codon Usage
	\| genetic code, codon degeneracy, codon usage, GC%		\| genetic code, codon degeneracy, codon usage, GC%
	\| CUTG table		\| CUTG table
	\| Frequencies of codons, grouped by amino acid; GC%		\| Frequencies of codons, grouped by amino acid; GC%
	\| Are synonymous codons uniformly used? What are the possible factors causing biased codon usages?		\| Are synonymous codons uniformly used? What are the possible factors causing biased codon usages?
			\|-
			\| Splicing Signal
			\| intron, exon, splicing, donor site, acceptor site, information
			\| 10 intron-exon junction sequences
			\| Information content (in bits) at each site
			\| Understand sequence logo
			\|-
			\| Phylogenetics Pipeline
			\| BLAST, alignment, phylogeny
			\| OspA sequence & Four Genome protein database
			\| A phylogenetic tree in PDF
			\| How to root a phylogenetic tree? How to test the statistical significance of a tree?
			\|-
			\| Transcriptomes of Two Cancers
			\| microarray, transcriptome, gene expression, fold change
			\| CCLE matrices of two groups of cancers
			\| A list of genes ordered by their significance in expression profile between the two cancer types; a heat map
			\| Pathway analysis of significantly expressed genes
	\|}		\|}
	----		----

imported>Weigang: /* May 8: Final Project (Session I) */

2013-05-05T17:42:28Z

May 8: Final Project (Session I)

← Older revision		Revision as of 17:42, 5 May 2013
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	# Formulate an outline of the final project report		# Formulate an outline of the final project report
	# Set milestones to be completed in a week		# Set milestones to be completed in a week
	* A suggested template for the final report		{\| class="wikitable"
	~~# Title Page~~		! Project
	~~## One page~~		! Biological Concepts
	~~## Title: One-line summary of methods and conclusion~~		! Computational inputs
	~~## Name & Date~~		! Computational outputs
	~~## Table of Contents~~		! Statistical analysis
	~~# Background & Introduction~~		\|-
	~~## One page, 1.5 line~~-~~spaced, size 12 font; '''worth 15 pts'''~~		\| Borrelia Codon Usage
	~~## 1st paragraph: Describe biological questions and objectives of your project~~		\| genetic code, codon degeneracy, codon usage, GC%
	~~## 2nd paragraph: Define and explain any biological terminologies you will use (e.g.~~, ~~ORF~~, codon, ~~transcription, intron, genome, etc)~~		\| CUTG table
	~~## 3rd paragraph: Summarize your approach~~		\| Frequencies of codons, grouped by amino acid; GC%
	~~## Unless it is your own opinion, use citations to indicate your information source and back up each~~ of ~~your statements and claims~~, ~~e.g., (Caserta et al. 2012)~~		\| Are synonymous codons uniformly used? What are the possible factors causing biased codon usages?
	~~# Materials & Methods~~		\|}
	~~## One page~~; ~~'''worth 10 pts'''~~
	~~## List~~ the ~~source of your input data (GenBank, etc)~~
	~~## Describe your computational algorithm (preferably with a flow chart)~~
	~~## Explain statistical methods~~
	~~# Results and Conclusion~~
	~~## One page; '''worth 10 pts'''~~
	~~## Show your program output as well as results of statistical analysis (e.g. with an R figure with legends)~~
	~~## Describe results~~
	~~## Draw your conclusions~~
	~~# Literature Cited~~
	~~## '''Worth 5 pts'''~~
	## Include Author, Year, Journal/Link URL, e.g., Caserta E, Haemig HAH,Manias DA, Tomsic J, Grundy FJ, HenkinTM, DunnyGM. 2012. In vivo and in vitro analyses of regulation of the pheromone-responsive prgQ promoter by the PrgX pheromone receptor protein. J. Bacteriol. 194:3386 –3394.
	~~# Appendix~~
	~~## '''Worth 10 pts'''~~
	~~## Attach your Perl/R scripts~~
	~~## Use the Carrier font and proper indentation~~
	----		----

imported>Weigang: /* May 15: Final Project (Session 2) */

2013-05-05T17:14:51Z

May 15: Final Project (Session 2)

@@ Line 507: / Line 507: @@
 ===May 15: Final Project (Session 2)===
 # Help debug your Perl/R scripts
 # Check your report outline
 # Set specific expectations for your final report
 ----

imported>Weigang: /* May 22: Final Project Due */

2013-05-02T20:09:19Z

May 22: Final Project Due

← Older revision		Revision as of 20:09, 2 May 2013
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	# <font color="blue">[Claimed]</font>(Phylogenetics) Write a BioPerl script to identify all variable sites given an alignment		# <font color="blue">[Claimed]</font>(Phylogenetics) Write a BioPerl script to identify all variable sites given an alignment
	# <font color="blue">[Claimed]</font>(Phylogenetics) Reconstruct ancetral sequences based on a phylogenetic tree. Identify evolutionary changes at each codon position and on each branch.		# <font color="blue">[Claimed]</font>(Phylogenetics) Reconstruct ancetral sequences based on a phylogenetic tree. Identify evolutionary changes at each codon position and on each branch.
	# (informatics) Compose a Perl script to calculate information content as intron-exon junctions		# <font color="blue">[Claimed]</font>(informatics) Compose a Perl script to calculate information content as intron-exon junctions
	* Project Ideas		* Project Ideas
	# Construct bioinformatics workflow using BASH/Perl/BioPerl		# Construct bioinformatics workflow using BASH/Perl/BioPerl