What Is The Best General Biobank Standalone/Gui Miner Tool ?

Question

[Manu Prestat]

Usually, in practical sessions, one of the first thing we teach as an introduction to bioinformatics for biologist students is how to access and retrieve sequence informations.

(I am surprised to be (if I'm not mistaken) the first one to ask a relative question as it is a central need to most of bioinformaticians and biologists that work with sequences :-) ).

As a personal experience, I used to explain how to proceed in two steps: first using the web, and second using the R program and some dedicated libraries.

But actually, I use a standalone program that has been developed in my PhD lab called QueryWin. Despite of its raw "look & feel" GUI, it's very convenient to combine several criteria to mine embl, genbank or swissprot. Moreover, this is the only one I know capable to split "parent sequences" into subsequences and vice-versa. To be honest, I did not really try other ones in depth as first it seems difficult to find, and second, I am used with this one.

I am wondering what the best standalone/GUI program design to that purpose. I know that a lot of interesting API exist for each well known databank (and by the way I use some of them too), but this is not the question here.

I'm sure some detailed answers could interest a lot of people in here!

and I profit of my first thread of the year to wish you a good one!

Answer 1

[Gjain]

MizBee-A Multiscale Synteny Browser

MizBee is a multiscale synteny browser for exploring conservation relationships in comparative genomics data. Using side-by-side linked views, MizBee enables efficient data browsing across a range of scales, from the genome to the gene.

Other stand alone programs in a suite:

• Galaxy
• Biological Magnetic Resonance Data Bank
• Scientific Databases and Tools from BioChemWeb.org
• The Database for Annotation, Visualization and Integrated Discovery (DAVID)

hope this is helps.

[Manu Prestat]

I'm sure this answer can be useful for some people, but I asked for standalone programs ;-)

[Gjain]

thanks. I get it ... we developed a suite for Chromosome conformation capture technology data: http://3dg.umassmed.edu/welcome/welcome.php

Answer 2

[Pierre Lindenbaum]

The NCBI Genome Workbench ?

NCBI Genome Workbench is an integrated application for viewing and analyzing sequence data. With Genome Workbench, you can view data in publically available sequence databases at NCBI, and mix this data with your own private data.

[Manu Prestat]

Thanks Pierre, I will give it a try.