Books on bioinformatics

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….

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

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

Homology – similarity: They’re DIFFERENT!!

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:

• Homology vs Similarity
• Degrees of similarity have different meanings
• Similarity vs Distance metrics

DNA-protein alignment

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.

Sequence alignments

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.

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!

Lab Humor

Just discovered Lab Bratz….. a comic strip about life in the lab.
Can empathize with this one!

The lab biosafety set are on the mark too… they start here!

Competition for EndNote?

I’ve used Reference Manager and EndNote over the years and have the latest version of EndNote (9 for Mac).
Can’t say they’re not useful, but I came across an Ad for SENTE (Mac only), which said:
“It’s like iTunes for academic literature”

Couldn’t resist! We tried the demo and like it enough to shell out a few $$ for a single license (3 machines).
So far the reports from the bench are very favorable.

One very cool feature is that you can DRAG a file (called 1471-2105-5-96.pdf) that you downloaded from a journal onto the SENTE entry for the article and SENTE will RENAME it something sensible like author name or title, e.g. Base-By-Base single nucleotide-level analysis of whole viral genome alignments.pdf
and then file it away for you.

SENTE seems to be under very active development. There’s nice HELP docs and a forum to ask questions.

Oh… and SENTE integrates into Microsoft Word and can import EndNote databases etc.

Smallpox virus – news!!

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

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.