Project Bioinformatics MOL075 2013-2014
First sit down and think about the research project. What is the meaning of the data?
What is the research question that you are going to answer? Where in this project
are you going to transfer information?
Your task
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We expect you to write, in teams of three students, a report of max 7 A4
(excluding appendices).
You will make the project report in this Word file. Do not use 2 columns text on
a page, use the full width of the page.
Hand in your report digitally at C.vanGelder@umcn.nl as a doc file (not a pdf!)
Deadline for report is 15 nov 2013, 9:00 hr.
Remember that the report needs to be printed to be corrected and graded, so
check that it can be printed!
General hints & remarks for the report:
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General remarks:
o Choose carefully what information is relevant to show, and how you want to show it. Use
figures, tables, pictures etc. to illustrate your results. You can for instance in the
Introduction paragraph show schematically the domains in a protein sequence.
o Don’t make your text a “bullet list” of results where the user has to draw his own
conclusions. You will take the reader by the hand and lead him through your text in a
story.
o Avoid constructs like “We ran BLAST to…and then we did this and then we did that, etc.
Write neutral texts: “Searches for homologs were performed with BLAST (version etc)”
o Try to be as clear and specific as possible. When talking about a certain amino acid
residue or mutation mention the protein involved, the residue name and the residue
number. Do not use words like “mutation number 1 has no effect”, but rather “the A127P
mutation has no effect”.
o In the text, when talking about specific amino acids, use the amino acid numbering
belonging to to the protein under study and not amino acid numbering related to
homologues. .
Figures and tables:
o should be functional, comprehensive, and nearly self-explanatory
o should be numbered and you must refer to them in the main text, otherwise no one will
read them.
o should always have a title and a legend explaining what is shown in those figures/tables.
o Should not contain things that have nothing to do with the goal of the figure
o Should contain labels when relevant
Copyright:
It is allowed to copy maximally 200 words literally from anywhere, provided you put double
quotes around it and you provide a reference to the source from where you copied it. This is the
only hard rule in this list of suggestions and the only rule that, if broken, results in 1 as your final
project grade.
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Title
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The report has a good title describing the topic of the study.
Authors
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List the authors here including student numbers.
Abstract
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The abstract will consist of a few sentences (max 7) where you summarise the main aspects of
the project:
Sentence 1 summarises the research question being solved in this project.
Sentence 2 summarises your approach.
Sentence 3 lists the main results/conclusion. Be specific here, do not use words like “mutation
number 1” but use the amino acid name and number to indicate a mutation
And that should normally be enough. If really needed, you can add a fourth sentence summarising
some discussion points.
Do not put literature references in the Abstract, nor tables or figures
Do not use the names of bioinformatics tools in the abstract, describe the approach/method not
the specific tools that you used.
Do not use swissprot and PDB codes in the abstract. Describe the protein and/or gene with its
proper name & species not by its code from a database.
Often, you will write the abstract after you have written the complete report, because it can be
easily distilled from the report text.
Introduction (maximally1,5 A4)
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The introduction should explain the question and provide the background information needed for
somebody of your own skill-level to understand what you have done to answer that question.
The things really needed in the introduction are:
1. The molecule & and its role in biology: what is it , where does it do what etc. Also describe
the important functional sites of the protein sequence and structure, like active site
residues, ligands, protein domain structure, known mutations and anything else you find
worth mentioning
2. The mutations investigated in this study, how were they found, what is their effect. You
may want to put in a table with the mutations, but this can also be part of the Results &
Discussion section.
Please use at least one Figure to illustrate an aspect of the biological function that you think is
relevant to show ..
You may want to use one or two pictures to illustrate the Introduction. Be careful to choose a
functional picture, not only a nice colourful image.
Methods ( ~ 0,5 A4)
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The report has a short Methods section where you describe the methods and tools used.
In principle, others should find enough information in the Methods section to allow them to repeat
your studies
Always start running your sequence with BLAST against the SwissProt database to discover if the
sequence is already known or to find close homologues of the protein. Study the information of the
proteins in the hit-list. You can use this info for your Introduction.
Do NOT put results or discussion in the methods section. You also do not discuss here WHY
you use certain tools, only HOW you use(d) them.
The following sentence is an example of a good sentence that you can use: “Searches for
homologs in SwissProt (version…) and PDB (has no version, so you cannot list it ) were
performed with MRS BLAST. The PDB file 1ABC was used for all studies, except blabla”.
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Put references to the tool and databases in the References section (and not in the Methods
text!). So do not put URLs in the Methods section. In the case of tools, you can use the website of
the tool as reference. Please include the version numbers of the databases and tools.
Use the right tool for the job. Use BLAST to search for homologues, use CLUSTAL for alignments.
So make sure not to use BLAST (which is a local alignment tool for fast database searching) but
CLUSTAL to make the crucial alignment in the Results & Discussion section..
When analyzing structure(s) use the WHAT IF servers (http://swift.cmbi.ru.nl/servers/html/) to:
1. List the sequence of a PDB file (Under Administration)
2. Analyze protein-cofactor contacts (Under Protein Analysis)
3. Analyze hydrogen bonds
Results & Discussion ( maximally 4 A4)
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In these sections the results of your study have to be described, including an explanation of the
strategy you used, the steps you took, etc. They also include the final results, i.e. the answers to
the biological question(s).
Run BLAST against the PDB database to find out if the structure of this protein is already known.
If the structure is not known, see if there is a file in the PDB that looks a lot like your protein and
that you can use to transfer information. If you have found one: Look at the structure of the protein
and try to understand what is going on
Important: If you are going to transfer information from one sequence to another: Indicate the %
identity and length of the alignment, and make clear if you are allowed to transfer information. Also
describe carefully from which sequence your are transferring information and which sequence you
are transferring information to.
Include a Figure showing the crucial alignment used for transfer of information! This figure
belongs here and not in the Appendix.
When showing an alignment:
1. you should use a proportional font, e.g. Courier, otherwise the amino acids will not line up
correctly.
2. make sure to have the names of the proteins in the alignment and not names like
“sequence 1” etc.
3. Think of ways to illustrate important amino acids in your alignment. Use colours, numbers,
boxes, labels, arrows etc. Be creative. Colour them and/or put a box around them. Also
put the residue number of important amino acids in the alignment.
4. skip useless data. If an alignment has been made to only find out if two sequences are
homologs, then you should not put the alignment in the report. But if an alignment was
made to transfer information from one sequence to another, an alignment is needed.
Be systematic. If you describe the mutations, name and describe them in the same order as you
mentioned them in the introduction (if you did). Feel free to add small but clear 3D pictures for the
mutations. If possible, combine two mutations in one picture.
When showing structures/ parts of structures:
o Don’t make pictures because they are nice, but because they make something clear to the
reader that you think is important to get clear
o Remove from pictures everything that does not add information useful for the point you
want to make
o In detailed pictures make sure to display the side chain atoms of the amino acids, not only
the backbone.
o When making pictures of molecules, use YASARA with a white background.
o Remove hydrogens if showing them is not relevant.
o Only label atoms or residues that you discuss in the text.
o Do not zoom in too much, do not zoom out too much, think about what you want to show
o Use colours only when needed to show something or to help the reader find a residue,
atom, interaction, etc., and not because they make the picture nicer.
Conclusion ( maximally1/2 A4)
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This is a short section containing the overall conclusion of your research. You can also talk about
things like potential weaknesses in your study, suggestions for follow-up research and anything
else you think should be discussed
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Acknowledgements
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If you want you can add Acknowledgements.
References
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Here you give a list of references. These are typically:
1. research papers
2. hyperlinks (to tools, databases & webservers).
For a research paper: Cite the literature reference. You may want to include the URL (e.g. of
PubMed) for the paper, but it should be preceded by the full literature reference!!
Example for reference to a research paper:
1. Joosten RP, Joosten K, Cohen SX, Vriend G, Perrakis A. Automatic rebuilding and
optimization of crystallographic structures in the Protein Data Bank. Bioinformatics
27:3392-8 (2011).
Make sure to reference to a paper in case you borrowed a picture from that paper.
Make sure that you quote the references in the text of the report
Please choose one method of referencing and use this method for all references.
Example of reference to tool or database:
1. Models were analyzed and results were visualized using YASARA View version 12.1
(http://www.yasara.org)
There is more out there than Wikipedia! Use more sources to gather information otherwise it will
cost you points.
Appendices
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Feel free to use Appendices but choose carefully what to put in the main text, what to put in an
Appendix, and what not to put in at all because you can also describe it in two sentences instead
of showing a large computer output.
Appendices contain additional information that is not required to follow the flow of the story you tell
in the report.
If you use Appendices make sure to refer to them in the main text, otherwise they will not be read
at all.
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