Template for report - WHAT IF servers

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Project Bioinformatics
MOL075 2012
-
2013

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



We expect you to write
, in
teams of t
hree

students
,

a report of
max 7

A4

(excluding appendices)
.



You will make the project report in th
is
Word file.
Do not use 2 columns text on
a page, use the full width of the page.



Hand in your report digitally at
verslagen@cmbi.ru.nl

as a doc file (not a pdf!)



Deadline for report is
15
nov 2012, 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:



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 ment
ion 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”
.



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
proj
ect
grade.



2


Title



The report has a
good
title describing the topic of the study.

Authors



List the authors here including student numbers.

Abstract



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 numbe
r 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



Often, you will write the abstract
after you have written the complete report, because it can be
easily distilled from the report text.

Introduction

(
maximally
1,5 A4)



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, 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 the
ir

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
.
.

Methods

( ~ 0,5 A4)



The report has a short Methods section where you describe the methods and tools used.



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 method
s

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 blab
la”.



Put
references to the
tool and databases

in the References section. In the case of tools, you can
use the website of the tool as reference.

Please include the version number
s

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 analy
zing 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


3.

Analyze hydrogen bonds

Results & Discussion

(
maximally

4

A4)



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 que
stion(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 yo
u 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. Colo
u
r 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 alignmen
t 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 informa
tion useful

for the point you
want to make

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 no
t 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

(
maximally
1/2 A4)



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

Acknowledgements



If you want you can add Acknowledgements.

References



Here you give a
list of references.

These are typically both research papers and
hyper
links
(
to
tools, databases & webservers
)
.

4




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.



For research articles: Please give the full literature reference and not only a PubMed link!



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).



Example of reference to tool or database:

4)
http://en.wik
ipedia.org/wiki/Snake_venom




There is more out

there than Wikipedia! Use more sources to gather information

otherwise it will
cost you points
.

Appendices



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 App
endices make sure to refer to them

in the main text, otherwise they will not be read
at all.