September 1, 2006

Books on bioinformatics

Filed under: Bioinformatics — cupton @ 1:01 pm

There’s a lot of choice these days if you want to learn something about bioinformatics….
People from biology or computer science are sure to find something useful here!

There’s even…. a Bioinformatics for Dummies.


Software as a Black Box….

Filed under: Bioinformatics, Science — cupton @ 12:58 pm

Why Biologists Should Not Treat Software as a Black Box….

On a similar theme to the last post.
Check out this link for a discussion by Dr. Joelle Thonnard.

EMBL-EBI’s Macromolecular Structure Database

Filed under: Bioinformatics, Science — cupton @ 12:57 pm

Somehow I managed to get signed up for the electronic version of:
OBBeC® Life Science Computing & Bioinformatics Magazine

I’m not really a big fan of electronic books and mags, but I thought I’d give it a try (beats getting a paper copy in the mail).

There’s a nice 4 page review of EMBL-EBI’s Macromolecular Structure Database (issue 12 p24).
It was easy to read on screen, and could quickly print off the review to hand around the lab.

You can subscribe to the mag here!

The issue also has a review of Leopard (the next version of OS X) and the new Apple X server smile.gif

August 16, 2006

Homology – similarity: They’re DIFFERENT!!

Filed under: Bioinformatics — cupton @ 12:28 pm

Just came back from a seminar which reminded me of this problem.

It’s not a tomMAYto : tomARto thing.

See these links for an explanation:

August 15, 2006

DNA-protein alignment

Filed under: Bioinformatics — cupton @ 9:41 pm

Have you ever wanted to align a protein sequence to a DNA sequence?

There a few reasons this can be useful….

Well, you can do it easily with NAP, developed by Xiaoqiu Huang, which allows also allows gaps in the alignment.

Huang, Methods for Comparing a DNA Sequence with a Protein Sequence, Computer Applications in the Biosciences 12, pp. 497-506, 1996.

We liked NAP so much we incorporated it into several of our tools (VOCs and VGO) with a JAVA interface. You can find our JAVA web interface to NAP here.

August 13, 2006

Sequence alignments

Filed under: Bioinformatics, Science — cupton @ 7:53 am

Have you ever wanted to make a small diagram to show a conserved motif or a sequence aligment?
And then pulled your hair out while trying to get it to look JUST THE WAY YOU WANT?
There’s a few programs to help, but most don’t quite have the flexibility or resolution.
I always used to use SeqVu, back in the pre OS X days.

Well, finally we (Cristalle Watson) made a stencil in OmniGraffle to easily build these diagrams. Attached Image

Yes, Omnigraffle costs $$.
Yes, it’s a manual process and may not be useful for big alignments.
BUT, it works!!

You can find our stencils at: Graffletopia – Science category!

August 12, 2006

Smallpox virus – news!!

Filed under: Bioinformatics — cupton @ 11:06 pm

A lot of poxvirus labs have been eagerly awaiting this research…
Genome Sequence Diversity and Clues to the Evolution of Variola virus
Science paper!

These genomes will be entered into the VOCs database as soon as they’re released to GenBank.

Snippet #2

Filed under: Bioinformatics — cupton @ 11:05 pm

A very nice weekend here in Lotusland BC (Victoria)…. unfortunately most of it was spent painting ceilings!
Where is Victoria? Have a look here:
Victoria Tourism

Snippet #2
Did you know that The Canadian Bioinformatics Help Desk produces a Newsletter that has a variety of useful Bioinformatics tidbits, including reviews of new software tools.
It’s supported by Genome Canada and is run out of Dr. David Wishart’s lab at the University of Alberta.
And you don’t have to be Canada for this Help Desk link to be useful.

August 11, 2006

Nothing ventured, nothing gained!

Filed under: Bioinformatics — cupton @ 9:22 pm

Well, this is the first entry… so welcome!
I’m not used to blogging, so no promises.

There seems to so much stuff out there on the Internet these days that one wonders why add to it?
Do we really need more cyberspace junk?
Do you really need another blog to read?

All I can promise is that I’ll add ONE useful snippet of bioinformatics/virus info in each post. It may be gathered from other blogs or sites… but that’s part of modern life (re-use, re-cycle, re-cover), or it may be novel (isn’t that what research is all about?).

Go look at Viral Bioinformatics-Canada.
This is a blatant plug for my site, but there’s all sort of useful bioinformatics tools there.
These will be highlighted here from time to time.
If you want a quick guide to the tools at the site… follow the News link to a series of PDFs.

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