Welcome to the JABBA menagerie: a collection of animal-themed, bogus bioinformatics names…that have nothing to do with animals!

Bioinformaticians make the worst zookeepers:

A

B

C

D

E

F

G

H

I

J

K

L

M

N

O

P

Q

R

S

T

U

V

W

X

Y

Z

 

Other suggestions welcome! Only requirements are that:

  1. The name is bogus, i.e. not a straightforward acronym and worthy of a JABBA award
  2. The acronym is named after an animal (or animal grouping)
  3. The software/tool has nothing to do with the animal in question

Great Scott! Five fun facts about DNA sequencing from 1985

As everyone is celebrating a certain 2015–themed calendar event today, I thought we could instead go back to the future past of DNA sequencing.

 

1.

Thirty years ago there were no automated sequencing machines. However, Sanger sequencing technology could still provide longer reads than most of Illumina's machines today, e.g. from this paper (A rapid procedure for DNA sequencing using transposon-promoted deletions in Escherichia coli):

The length of the sequence that could be read from each gel in a single run varied from 175 to 200 nt.

 

2.

The idea of sequencing nuclear genomes was still largely a pipe dream, but smaller genomes were tractable. 1985 saw the addition of the Xenopus laevis mitochondrial genome to the tiny collection of organelle genome sequences. Figure 3 of this paper displayed the full sequence, spread over six pages that looked like this:

Including long DNA sequences in journal articles was a surprisingly common practice at this time.

 

3.

There were two releases of GenBank in 1985. The second release saw the database grow to an astounding set of 5,700 sequences, totalling 5,204,420 bp. For comparison, this year also saw the release of the Commodore 128 home computer which came with 128 KB of RAM. The first 3.5" hard drives were only a couple of years old, and could store 10 MB (so capable of storing the DNA sequences in GenBank, but possibly not the associated annotation).

 

4.

The SEQ-ED program was published, allowing the handling of 'long DNA sequences' that were 'up to 200 Kbp'.

 

5.

Somewhat amazingly, people were writing bioinformatics software for Apple computers. The journal CABIOS included this paper:

But how did people distribute software in the days when there was no GitHub, SourceForge, or indeed…no world wide web?

For both code and source of PEGASE, please send two blank 5" diskettes and indicate precisely your system configuration (there is a slight difference between the Apple II+ and the Apple lIe version which depends on the availability of lower case characters).

BINGO, DINGO, PINGO, RINGO, and SPINGO

Dovetail takes flight [Link] →

If you ever want to know about the latest developments in sequencing, you owe it to yourself to follow Keith Robison's blog. In his latest post he talks about the launch of the new de novo assembly service from Dovetail Genomics. Keith concludes:

Personally, a pure service offering is very attractive, since that means not having to find internal resources to learn the new technology and then execute on it. I checked with Dovetail, and while I don't have $40K burning a hole in my pocket, if I did I could grab something out of the garden or from the local seafood market, I really could have a complex genome scaffold of my very own in about two months. That's an exciting vision, and perhaps will be a major force in the sunsetting of science's tolerance for highly fragmented draft genomes.

Readers may also enjoy Bio-IT World's report on this new Dovetail service.