Hey, don't sweat the small stuff, man. Why should you be expecting a perfect match? Do you expect Sanger people to be perfect? DO you expect the guy who deposited the DNA sequence in Genbank or Swissprot to be perfect? Do you expect the experimental techunique used in the sequencing to be perfect? Do you expect the DNA sequencing enzyme used in the automated DNA sequencing to be perfect? Do you expect Nature to be perfectly identical when it comes to replication? Do you expect 100% fidelity when it comes to the polymerase activity (otherwise, why would you expect mismatch repair enzyme? well to correct for these mistakes in the replication process, and even then, they are not perfect in correcting the errrors, and that's where mutations come in.)?

Here are some of the possible reasons:

1. Strain and Individual Differences There are so many different strains of B. pseudomallei If you look at IVLE discussion forum, a student has posted the taxonomic tree of Burkholderia, and that includes quite a number of B pseudomallei species and strains. Not all the strains are identical, and at the genomic level, there are bound to be differences. In fact, between individuals, we would expect variations, as much as you and I are both human beings, but you can be very sure, my DNA sequence is not the same as yours. And you may have studied this, SNP (Single Nucleotide Polymorphism) among other types of genetic variations amongst individuals accounts for why we differ from each other. So mismatches here could mean somebody sequenced a different strain from the guys who sequenced the genome.
2. Sequencing Imperfection Alternatively, it could be the incompetence of the guy who read the sequencing gel, or the automated sequencing gel reader throwing up an ambiguous peak, which the software made a wrong guess, or the enzyme's fidelity in reproducing the sequence, or simply a typographical error somewhere.

There is no need to delete any file. If you wish to reuse the filename, just take the right file contents, and name it with this filename, and upload it. The system will overwrite the wrong file with the new file containing the correct contents. If you are not going to reuse the filename, just leave it there, or upload a blank file with the same filename.

Note taking is important during the course of the work. Good researchers keep a electronic log of what they did, so thay do not forget where they obtained their data and results. Our personal experience is that if you do not keep a log, then you will definitely forget it. That is why we usually keep a electronic text file of the steps that we take in this kind of work. In this way, not only can you yourself repeat the work and satisfy yourself that your work is reproducible, others too can also reproduce your results if you share with them your notes. This applies both in bioinformatics projects as well as in all scientific research projects in the laboratory. Always note down observations and details of what you did and found.

There are many ways of doing it. For example:

Blastp was performed using the web service at 
http://www.ncbi.nlm.nih.gov/blast using the protein XXX (accession no. 
XXXXXXX) as the query. The standard default parameters provided were used 
(or other alternatives which you should state clearly) with the 
sole change being the turning off of the low complexity filter to increase 
the sensitivity of the search. X hits were obtained, of which Y were 
retained based on a E-value cutoff of 0.0001. The GenBank files and the
alignment of these hits were then examined by visual inspection and 
the following hits selected:

Accession no.	Gene name	Reason for selection
xxx		xxx		xxx"

This practical is not about building a website or a webpage. We are merely using the web as a convenient method for sharing and publishing your findings. So if you can just write up the report in a Word document, and save as HTML, and the data contains earth-shaking findings :-), that will be good enough. Alternatively, you can use Microsoft FrontPage, Netscape Composer, Dreamweaver etc all of which are accessible under NUSNET Windows Shopping.

There is no need to have javascript or flash animation or fancy colours although you might like to do it as a challenge, but you should not waste too much time on it unless it is a hobby to you.

You can check up the taxonomy section of Genbank, or search the literature for papers that pertain to the classification of Burkholderia based on your skills learnt in the first part of the LSM2104 course, of course.

During your practical sessions, your TAs will be guiding you on this.

By all means learn to cooperate with each other, share results, discuss findings etc. But for the purposes of the continual assessment, of course, you will be graded according to your findings, and how well you incorporate shared findings into your report in your own unique way. And findings that are reported and that are identical (word for word sometimes!) to all your partners in the group without any unique saving features that are unique to yourself would look pretty bad on you, wouldn't it? The TAs grading your work will be wondering if you did nothing and copied everything from somebody else, or vice versa, and then, in their doubtful minds about you or your team's work, then, your grades may well be doubtful too, wouldn't they? The question is how much data can you jointly share with your team members. Discuss it with your TAs depending on the circumstance.

You should. Those are the sessions where you can ask questions and be guided on what to do in case of some interesting results. It is also a time where you can discuss with your fellow members of your team (if you have one assigned). It should be the time you do your practical mini-project, unless you want to do them at home. Note that some techniques which you have to apply in the practical mini-project may come much later in the lecture series, and you may have questions about how to apply them, or we may have some interesting tips for you. Of course, we will try to post them to the IVLE site, but why not turn up?

If you are very efficient, you may have completed everything way beforehand. Well, then it is up to your discretion whether to come or not.

You can use a number of ways, eg. from JEMBOSS http://sf01.bic.nus.edu.sg/jemboss/. Your TAs will be there to assist. Alternatively, request for a Web accessible system to do this specifically for the Genome.

You should be able to find out yourself, but for the practicals, we will put up a local site for your convenience. You will be informed about the local site in due course. If not, ask for it.

All lecture notes and web links are (or will be) available from the website: http://everest.bic.nus.edu.sg/lsm2104 and on the IVLE system. You shouldn't need to print them out as printing hardcopy is an outmoded way of revising your notes. Every thing today is in the online mode. It would be helpful if you could upgrade to online modes of learning.

Again as in FAQ2, it is the <A HREF=blah.blah.html> messing up. Check that you have named your files according to your own name, eg tanahbeng.html tanahbeng2.html tanahbeng3.html.

Then, look in the HTML file that calls these missing files. Look at the referring hyperlink. <A HREF=tanahbeng2.html> or not?

If not, there must be some rubbish in front of tanahbeng2.html eg H://stupiddirectory/tanahbeng2.html DELETE those unnecessary ABSOLUTE URL and substitute with the RELATIVE URL, which is just tanahbeng2.html, without anything else. <A HREF=tanahbeng2.html> my next files </A>

First, make sure you name your image gif/jpg files according to your name eg. tanahkow1.gif, tanahkow2.gif etc, BEFORE you upload the files.

Second, make sure upload them to the server using the prescribed way.

Third, open your HTML files with NOTEPAD, and take a look at where your IMG SRC references are. Check that you are using RELATIVE links. This means you DO NOT use ABSOLUTE URLs, ie. you DO NOT use http://blah blah/blah blah/student/tanahkow2.gif. IT WILL FAIL when I move the file in the frozen directory somewhere else.

Use RELATIVE links instead... JUST tanahkow2.gif, as simple as that. For every link that causes a problem, open up your HTML file and edit the offending line containing the IMG SRC reference and delete the unnecessary URL path leaving behind ONLY the filename.

You can do the basic minimum and still pass. But check your minimum first with your TAs just to make sure. Generally, most students tend to overdo. Always aim for efficiency... minimum work, maximum effect.