BIO Assignment 3 2011

   

Assignment 3 - Multiple Sequence Alignment

Please note: This assignment is currently inactive. Unannounced changes may be made at any time.  

 

Introduction

A careful multiple sequence alignment is a cornerstone for the annotation of a gene or protein...

Preparation, submission and due date

Read carefully. Be sure you have understood all parts of the assignment and cover all questions in your answers! Sadly, we always get assignments back in which people have simply overlooked crucial questions. Sadly, we always get assignments back in which people have not described procedural details. If you did not notice that the above were two different sentences, you are still not reading carefully enough.

Prepare a Microsoft Word document with a title page that contains:

• your full name
• your Student ID
• your e-mail address
• the organism name you have been assigned (see below)

Follow the steps outlined below. You are encouraged to write your answers in short answer form or point form, like you would document an analysis in a laboratory notebook. However, you must

• document what you have done,
• note what Web sites and tools you have used,
• paste important data sequences, alignments, information etc.

If you do not document the process of your work, we will deduct marks. Try to be concise, not wordy! Use your judgement: are you giving us enough information so we could exactly reproduce what you have done? If not, we will deduct marks. Avoid RTF and unnecessary formating. Do not paste screendumps. Keep the size of your submission below 1.5 MB.

Write your answers into separate paragraphs and give each its title. Save your document with a filename of: A3_family name.given name.doc (for example my first assignment would be named: A3_steipe.boris.doc - and don't switch the order of your given name and familyname please!)

Finally e-mail the document to [boris.steipe@utoronto.ca] before the due date.

Your document must not contain macros. Please turn off and/or remove all macros from your Word document; we will disable macros, since they pose a security risk.

With the number of students in the course, we have to economize on processing the assignments. Thus we will not accept assignments that are not prepared as described above. If you have technical difficulties, contact me.

The due date for the assignment is XXXXX at 10:00 in the morning.

Grading

Don't wait until the last day to find out there are problems! Assignments that are received past the due date will have one mark deducted at the first minute of every twelve hour period past the due date. Assignments received more than 5 days past the due date will not be assessed.

Marks are noted below in the section headings for of the tasks. A total of 10 marks will be awarded, if your assignment answers all of the questions. A total of 2 bonus marks (up to a maximum of 10 overall) can be awarded for particularily interesting findings, or insightful comments. A total of 2 marks can be subtracted for lack of form or for glaring errors. The marks you receive will

• count directly towards your final marks at the end of term, for BCH441 (undergraduates), or
• be divided by two for BCH1441 (graduates).

   

Retrieve

   

In Assignment 2 you had retrieved the Saccharomyces cerevisiae Mbp1 protein sequence. Here I have compiled the most similar homologue from the organisms you have studied:

Source sequences

 

In your second assignments, the following proteins have been found as the best matches to the yeast Mbp1 protein:

Organism	CODE	GI	Refseq	Uniprot Accession	Most similar yeast gene
Aspergillus fumigatus	ASPFU		Refseq	Accession	Yeast
Aspergillus nidulans	ASPNI		Refseq	Accession	Yeast
Aspergillus terreus	ASPTE		Refseq	Accession	Yeast
Candida albicans	CANAL		Refseq	Accession	Yeast
Candida glabrata	CANGL		Refseq	Accession	Yeast
Cryptococcus neoformans	CRYNE		Refseq	Accession	Yeast
Debaryomyces hansenii	DEBHA		Refseq	Accession	Yeast
Eremothecium gossypii	EREGO		Refseq	Accession	Yeast
Gibberella zeae	GIBZE		Refseq	Accession	Yeast
Kluyveromyces lactis	KLULA		Refseq	Accession	Yeast
Magnaporthe grisea	MAGGR		Refseq	Accession	Yeast
Neurospora crassa	NEUCR		Refseq	Accession	Yeast
Schizosaccharomyces pombe	SCHPO		Refseq	Accession	Yeast
Ustilago maydis	USMA		Refseq	Accession	Yeast
Yarrowia lipolytica	YARLI		Refseq	Accession	Yeast

 

• Download sequences and generate multi-Fasta file

 

In addition, the following proteins have been found to have significant sequence similarity to the yeast Mbp1 APSES domain:

List ...

• GI
• EBI
• Most similar yeast gene

 

• For all these proteins APSES domains plus Mbp1 homologues, perform a batch search of the APSES domain, as represented in the SMART database ...
• using the domain boundaries defined by SMART, generate a multi-Fasta file of all APSES domains. your header lines should contain a five letter code for the organism, the name of the most similar yeast gene and the starting and ending amino acid number from the source sequence. It should NOT contain any non-alphanumeric character except for the starting ">".

Orthologues

 

Instruction

 

• Task

 

Instruction

 

• Task.

APSES domains

 

Instruction

 

• Task

 

Instruction

 

• Task.

   

Align

   

SUB section Heading (X marks)

 

Instruction

 

• Task

 

Instruction

 

• Task.

   

Analyse

   

SUB section Heading (X marks)

 

Instruction

 

• Task

 

Instruction

 

• Task.

   

[End of assignment]

If you have any questions at all, don't hesitate to mail me at boris.steipe@utoronto.ca or post your question to the Course Mailing List