BISC219/F12: Assignment Series2 DNA Sequencing

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
(New page: {{Template:BISC219/F12}} <div style="padding: 10px; width: 720px; border: 5px solid #7E354D;"> ==DNA Sequencing Analysis- 10 points== Please follow the instructions in the wiki in Lab6 S...)
(DNA Sequencing Analysis- 10 points)
Line 5: Line 5:
Please follow the instructions in the wiki in Lab6 Series2 for using the DNAStar analysis software to compare the DNA sequences provided for the mutated and wild type versions of the gene we have located and identified as associated with your Dpy phenotype in our forward genetics project. Once you have discovered the exact nature and extent of the mutation in  the gene of interest in''C. elegans'', you are to look for and investigate homologs/orthologs in other species. The directions for using the DNAstar software by Lasergene to analyze your sequences are found at: [[Media:Instructions for DNA sequence analysis_1.doc]]<BR><BR>
Please follow the instructions in the wiki in Lab6 Series2 for using the DNAStar analysis software to compare the DNA sequences provided for the mutated and wild type versions of the gene we have located and identified as associated with your Dpy phenotype in our forward genetics project. Once you have discovered the exact nature and extent of the mutation in  the gene of interest in''C. elegans'', you are to look for and investigate homologs/orthologs in other species. The directions for using the DNAstar software by Lasergene to analyze your sequences are found at: [[Media:Instructions for DNA sequence analysis_1.doc]]<BR><BR>
-
Please write a Results section, a narrative '''with at least one figure or table''', and a separate Discussion on this sequence analysis (not the whole forward genetics investigation), addressing its implications. '''The figure should ''NOT'' be a screen shot of the sequences and amino acids from DNAStar™, '''but rather, something of your own design. (Remember that the screen shot of the polypeptide sequence may show misinformation if there is a stop codon that does not indicate the end of translation.) The assignment is about the DNA sequencing analysis exclusively and does not include other findings from this project. This graded exercise will allow us to give you feedback on how well you can differentiate "what goes where", eg. results vs. discussion. There should be a properly formatted Literature Cited page with references cited in the format of the journal ''Genetics.'' Citation of functional information gleaned from authors who contributed information to WormBase should be attributed to the original published investigation. Information on citing WormBase can be found at [http://wiki.wormbase.org/index.php/Citing_WormBase | Citing Wormbase].  
+
Please write a Results section, a narrative '''with at least one figure or table''', and a separate Discussion on this sequence analysis (not the whole forward genetics investigation), addressing its implications. '''The figure should ''NOT'' be a screen shot of the sequences and amino acids from DNAStar™, '''but rather, something of your own design. (Remember that the screen shot of the polypeptide sequence may show misinformation if there is a stop codon that does not indicate the end of translation.) The assignment is about the DNA sequencing analysis exclusively and does not include other findings from this project. This graded exercise will allow us to give you feedback on how well you can differentiate "what goes where", eg. results vs. discussion. There should be a properly formatted Literature Cited page with references cited in the format of the journal ''Genetics.'' Citation of functional information gleaned from authors who contributed information to WormBase should be attributed to the original published investigation. Information on citing WormBase can be found at: [http://wiki.wormbase.org/index.php/Citing_WormBase Citing Wormbase].  
Remember that ''your'' experimental work in this investigation should be the central focus of your discussion (don't write a research review!), although the analysis of the significance of your findings should be integrated with those of other outside studies. The goal of the discussion is to expand your reader's understanding of the significance of the ''dpy'' gene  that you have characterized in your forward genetics project. It should include the importance of this gene and gene product in ''C. elegans'' and in other species. This information about homologs should not be written as a 'laundry list'. The sum of information about this gene or gene product in other species should be examined for commonality and for import, perhaps as evidenced by evolutionary conservation or for functional significance of the gene product. If there are no homologs, what might that mean? This assignment is due at the beginning of Lab 7. <BR><BR>
Remember that ''your'' experimental work in this investigation should be the central focus of your discussion (don't write a research review!), although the analysis of the significance of your findings should be integrated with those of other outside studies. The goal of the discussion is to expand your reader's understanding of the significance of the ''dpy'' gene  that you have characterized in your forward genetics project. It should include the importance of this gene and gene product in ''C. elegans'' and in other species. This information about homologs should not be written as a 'laundry list'. The sum of information about this gene or gene product in other species should be examined for commonality and for import, perhaps as evidenced by evolutionary conservation or for functional significance of the gene product. If there are no homologs, what might that mean? This assignment is due at the beginning of Lab 7. <BR><BR>

Revision as of 10:49, 16 August 2012

DNA Sequencing Analysis- 10 points

Please follow the instructions in the wiki in Lab6 Series2 for using the DNAStar analysis software to compare the DNA sequences provided for the mutated and wild type versions of the gene we have located and identified as associated with your Dpy phenotype in our forward genetics project. Once you have discovered the exact nature and extent of the mutation in the gene of interest inC. elegans, you are to look for and investigate homologs/orthologs in other species. The directions for using the DNAstar software by Lasergene to analyze your sequences are found at: Media:Instructions for DNA sequence analysis_1.doc

Please write a Results section, a narrative with at least one figure or table, and a separate Discussion on this sequence analysis (not the whole forward genetics investigation), addressing its implications. The figure should NOT be a screen shot of the sequences and amino acids from DNAStar™, but rather, something of your own design. (Remember that the screen shot of the polypeptide sequence may show misinformation if there is a stop codon that does not indicate the end of translation.) The assignment is about the DNA sequencing analysis exclusively and does not include other findings from this project. This graded exercise will allow us to give you feedback on how well you can differentiate "what goes where", eg. results vs. discussion. There should be a properly formatted Literature Cited page with references cited in the format of the journal Genetics. Citation of functional information gleaned from authors who contributed information to WormBase should be attributed to the original published investigation. Information on citing WormBase can be found at: Citing Wormbase.

Remember that your experimental work in this investigation should be the central focus of your discussion (don't write a research review!), although the analysis of the significance of your findings should be integrated with those of other outside studies. The goal of the discussion is to expand your reader's understanding of the significance of the dpy gene that you have characterized in your forward genetics project. It should include the importance of this gene and gene product in C. elegans and in other species. This information about homologs should not be written as a 'laundry list'. The sum of information about this gene or gene product in other species should be examined for commonality and for import, perhaps as evidenced by evolutionary conservation or for functional significance of the gene product. If there are no homologs, what might that mean? This assignment is due at the beginning of Lab 7.

Grading Rubric

Results & Discussion Rubric- DNA sequencing Analysis – 10 points

At or Above Standard Below Standard Possible
Points
Points

Earned

Data Analysis Narrative is structured appropriately: begins with a concise description of topic, experimental goals and experimental design. Narrative references figures & tables directly and describes key findings accurately, concisely and clearly & includes only relevant information. Data analysis is thorough and leads incrementally & clearly to appropriate conclusions to experimental question and addresses topic’s goals. Analysis is understandable to an audience unfamiliar with topic and principles used in the experimental design. Narrative doesn't begin with an appropriately concise description of the experimental goals and experimental design. Narrative omits key findings, describes the data inaccurately or unclearly, includes irrelevant information, or is repetitive. Narrative fails to give appropriate conclusions to the experimental questions or fails to show how the experimental data allow the conclusions. Specific figure and table numbers for data that support conclusions is not cited in the narrative. Data analysis requires background knowledge that general audience may not have. 2.5 __/2.5
Table(s)
&/or Figure(s)
Table(s) and/or Figure(s) well designed to illustrate conclusions and give the main point visually and easily. Included all crucial information that allows the figure or table to make the main points visually and to “stand alone”. All data adequately identified; labeling appropriate. Title and Legend information properly placed and appropriate. Figure(s) or table(s) not well designed to illustrate main points visually, clearly, or in most direct and simple way or missing essential information needed for understanding. Title and Legend information not appropriate or not properly placed 2.5 __/2.5
Discussion Discussion begins with a brief restatement of topic & experimental goals and a summary of the main findings in the results section with specific references to Fig. or Table # for the data referenced. Discussion uses outside sources that are properly cited in the format requested (model journal Genetics)in the body of the discussion and in an included Works Cited page. (Note that citation of functional information gleaned from WormBase or other public databases should be to the published original investigation rather citing Wormbase.) Your work in this investigation is the central focus although it is integrated with other outside studies in order to expand your reader's understanding of the significance of the dpy gene that you have characterized in your forward genetics project. Discussion includes the importance of this gene and gene product in C. elegans and in other species. Discussion was not properly structured, did not include properly cited sources, was missing a Works Cited page or the page was formatted incorrectly. Discussion did not center around and specifically reference your findings or did not expand the scope and significance of the investigation with appropriately integrated information from outside sources. 5 __/5
Total 10 __/10



Personal tools