
Show HN: Web app for DNA sequence manipulation and PCR Primer design - folli
http://genewarrior.com
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kevinwuhoo
This is really cool! In my experience, few scientific tools are designed with
modern interfaces. Most are a webpage with many, many inputs and textareas and
some expectation of the user to understand or trust the defaults (looking at
you BLAST [1]). I haven't designed a primer in quite a while, but doing a
cursory Google search for "primer design" confirms that things haven't changed
much.

I know that writing and maintaining user authentication code can be quite a
slog, but have you though of making a private/paid version of this? I can see
a few times where something like this could be useful. Ex: assembling a number
of sequences, annotating them, and having all that metadata inline to share
with colleagues? Maybe having some kind of Jupyter Notebook inoperability
would be enough?

[1]:
[https://blast.ncbi.nlm.nih.gov/Blast.cgi](https://blast.ncbi.nlm.nih.gov/Blast.cgi)

~~~
whistlerbrk
About ten years ago I started down this path myself, it just seemed
overwhelming though to recreate all the functionality of the desktop systems
like Vector NTI on the web. With today's tools it is likely much better. It
does seem as you're alluding to though that a Jupyter like format would work
really well. I wonder what the state of the art is today at least on desktop.

~~~
jfarlow
Unfortunately, software has not much advanced beyond where it was ten years
ago. There have been a lot of attempts, but the fact is that it's very
difficult to see returns on mass-market scientific software - the market is
relatively small compared to the likes of Snapchat. The software tooling
certainly makes it easier to make the scientific tools - but you still have to
earn enough to support a company (and compete against 'decent' freeware).
Desktop software - outside of very custom huge pharma-style companies, or
free-ware academic python libraries is a non-starter - as no one will download
it.

The nicest Desktop software I know of is SnapGene:
[http://www.snapgene.com/](http://www.snapgene.com/) which has to compete
against the ancient (and pretty good) freeware, APE:
[http://biologylabs.utah.edu/jorgensen/wayned/ape/](http://biologylabs.utah.edu/jorgensen/wayned/ape/)

On the web there is YC's own Benchling:
[https://benchling.com/](https://benchling.com/)

Twist (Startup DNA synthesizer) just bought Genome Compiler:
[http://www.genomecompiler.com/](http://www.genomecompiler.com/)

Teselagen for those hardcore genetic engineers:
[https://www.teselagen.com/](https://www.teselagen.com/)

Our own Pinecone: [https://serotiny.bio/](https://serotiny.bio/) (styled to be
a 'simple' abstraction above the DNA to produce functional proteins while
bypassing cloning)

And Desktop Genetics (for CRISPR design):
[https://www.deskgen.com/](https://www.deskgen.com/)

The older players (VectorNTI, and-the-rest-I-can't-rememeber) are never
updated and likely yet exist to service contracts from huge institutional
customers.

It's a relatively small (and dispersed) community of users right now. We need
a place that scientists actually go to to show off all of our nice shiny new
toys. Each comes with their own style and with their own strengths - it'd be
fun to showcase them all together.

~~~
jfarlow
Just because it's funny - direclty from Vector NTI's FAQ on their webpage,
today, in April 2017:

1\. When is Vector NTI Advance™ 11.5 available? Version 11.5 was launched on
October 15, 2010.

2\. Is Vector NTI Advance® 11.5 compatible with Microsoft® Windows 7? Yes.
Version 11.5 is compatible with Windows 7 on 32-Bit Systems - 64-Bit
compatibility is currently in development.

3\. Is Vector NTI Advance® 11.5 compatible with Mac OS? Yes, this requires Mac
OS® X running Windows® under Parallels Desktop® 5 or Boot Camp.

[https://www.thermofisher.com/us/en/home/life-
science/cloning...](https://www.thermofisher.com/us/en/home/life-
science/cloning/vector-nti-software/vector-nti-advance-software/vector-nti-
frequently-asked-questions.html)

~~~
kevinwuhoo
That's absurd! Still the same version I was using when I was in grad school.
I've heard that Benchling is a decent alternative. Although few, if any,
companies have the marketing and sales resources as Thermo.

------
jfarlow
Nice work. Getting all of these tools in one place, in an easy to use way is
not always easy. I'm well aware of what goes on behind the scenes to make
something like your alignment there as straightforward to use. The tricky part
is what next :)

I'm curious what your plans are - interoperability, private infrastructure,
plugins/extensibility for others or just simply nice tools for people to use.

I'd also be curious how you intend to approach the differences and
distinctions between protein and DNA sequences. It doesn't look like you
currently have much to do with an amino acid sequence. At Serotiny we've
chosen to focus on the amino acid sequences for manipulation and leave the DNA
in the background. It feels like it's often a trade-off - either/or. It's a
challenge to get both into the same working environment without overwhelming
the user.

I'd be curious your thoughts on what we've built:
[https://serotiny.bio](https://serotiny.bio)

btw - it's nice to see some ShowHNs show up for biological software.

~~~
folli
Thanks for the encouraging words! I don't have any future plans yet, depends
on the feedback I get and if there's enough interest for further features.

I think you're touching a valid point, but it goes even further. There are
many different use cases for a bio-software; a bench-worker has different
requirements than a geneticist, microbiologists vs cell biologists etc, WGS
and RNA-seq need an even more different toolset. It's impossible for a single
software to cover all possible aspects of biology. The only thing you can do
is focus on one group of users and try to fullfill their requirements.

~~~
jfarlow
yep :)

Unfortunately, the dearth of tools means everyone (coming from as many
directions) feels like they must rebuild every tool - so there is a bit of a
convergence right now - which spreads every tool thin. But the market for
'RNA-seq tools' is but a fraction of 'biochemical scientists', which itself is
still a 'tiny' market to produce high-tech software for.

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etimberg
Cool! I built something similar to the find tool for a friend. However, it's
for RNA and specifically for looking for a region that could base pair as part
of an RNA secondary structure interaction. It allows you to search for all
possible locations that could pair given a certain number of mismatches.

It can also correlate against MFOLD predicted RNA secondary structures to
eliminate possibilities that are not in single stranded regions.

Tool: [http://everttimberg.io/app/rna/](http://everttimberg.io/app/rna/)

~~~
folli
Nice tool! I also was planning to integrate Mfold into the toolset. However I
put it on hold due to lack of time.

------
bhickey
Thanks, better tools are a godsend. Back in school I spent too much time using
PrimerX
([http://www.bioinformatics.org/primerx/](http://www.bioinformatics.org/primerx/)).

------
JohnJamesRambo
I can't wait to use this to create phylogenetic trees when I need some. Thanks
for posting!

~~~
folli
Be aware that this is a quick-and-dirty way to get a tree. It's based on the
MUSCLE guide tree to get a quick glimpse. It doesn't replace a real
phylogenetic tree algorithm such as RAxML.

