Jing et al
Thank you for the offer to write some code to help advance the
metagenomics arena. It is certainly needed.
So the problem is well known with megablast and shotgun metagenomics and
without proper understanding and correct software will yield very
misleading and in many cases incorrect data. For those of us who wish
NOT to move to a protein level of comparison for specific reasons, we
are stuck.
*The Problem:*
If I megablast 50 million sequences from a HiSeq run, millions of rRNA
sequences will have a 99% match to all microbes rRNA genbank deposits.
Not surprizing since the rRNA is highly conserved. The difference
between E.coli and Shigella is 1 to 2 bases for the full 1540 bp 16s.
So 16s is not useful for Genus level, and certainly not Species
*So what happens:*
The returned matches will have many hits to whatever model organism is
in Genbank. For example E coli has 13000 entries for rRNA and
Sphearotilus has 3 entries for rRNA. If the blasted sequence matches
both, the results will mislead the investigator to think they have 13000
hits to E coli, EVEN if the microbe is Sphearotilus.
*The cure?:*
If there was a way to filter/ remove all hits ? Let say, for example,
that a result has a first match (say E. coli) at >99% a second match
(say Pseudomanas) at >99% and a third , forth and fifth match >99 for
three other organisms. This sequence _must_ be discarded because it is a
conserve sequence.
Basically conserved sequence is the enemy and invalidates the entire
result.
*
**Another problem:*
If you have a reference sample with 19 non-model microbes, and you run
that by HiSeq Shotgun for metagenomics and then megablast, what do you
think you get? If E coli is not in the reference sample, how many hits
do you think you get? Yes, 10,000 of thousands. So without removing
conserved sequences, your data is wrong and you are much better served
by culturing and running a Biolog metabolic panel and comparing to the
sequence result.
So where do we start? I have some shotgun metagenomics data from the
reference sample which included the 19 microbes. That was data from a MiSeq.
Scott
Scott Tighe
Senior Core Laboratory Research Staff
Advanced Genome Technologies Core
University of Vermont
Vermont Cancer Center
149 Beaumont ave
Health Science Research Facility 303/305
Burlington Vermont 05405
802-656-2557
On 9/20/2013 9:17 PM, Jing Yu wrote:
> Hi Scott,
>
> I can do some perl programming, such as local/remote blasting. Can you
> specify your problem a little bit clearer, so that maybe I can write a
> program to do just that?
>
> Regards,
> Jing
>
>
>
>
> Gerald
>
> 16s is basically useless for identification to genus. Since I started
> sequencing 16s in 1992, I have come to realize that without sequencing
> the full 1540 bases, it is generally misleading, and even than, it is
> not accurate enough to nail genus on more than 1/2 the cases.
> However, what is your feeling on ITS and gyrase, They seem to be far
> more discriminating but those databases have been decommissioned
> sometime ago.
>
> The desirable thing would be that Galaxy or NCBI add a "filter
> conserved genes" [ ie any hit with a second choice greater than 3%
> distance]. Something such as that.
>
> If you (or others) are aware of such a thing, I'd love the here about it.
>
> Sincerely
> Scott