Scott,
agreed, 16S is not accurate if you only have partial sequences. I would make 
the Galaxy button(s) more specific, saying "remove all rRNA and tRNA genes from 
bacteria/archaea/eukaryotes". That would leave the user with protein coding 
regions and intergenic regions. Ideally, one would then add an option "compare 
to gene collection" which would then give options for a collection of gyrase 
etc. As the gyrase collection is no longer available, one would have to rebuild 
this from the sequenced genomes - that's far from perfect in terms of coverage, 
but at least the quality of the published genomes is generally good (rRNA gene 
sequences are often not very good, another problem with the rRNA approach). 
Currently, I don't know of a such a program.
 
Gerald



From: Scott Tighe <scott.ti...@uvm.edu>
>To: Gerald Bothe <g_bo...@yahoo.com>; galaxy-user@lists.bx.psu.edu 
>Sent: Thursday, September 19, 2013 10:45 AM
>Subject: Re: [galaxy-user] Metagenomic filtering
>
>
>
>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
>
>
>
>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
802-656-2557On 9/18/2013 2:05 PM, Gerald Bothe wrote:
>
>Removing model organisms may not be enough, you may have the same problem 
>with, say, a Clostridium cluster IV anaerobe. I think a solution would be to 
>> 
>>first: compare to a collection of genes, e.g. get all the hits for 16S rRNA 
>>genes, RNA polymerases (conserved to quite conserved), and to e.g. ion 
>>channels and cell surface proteins. 
>> 
>>then: once a read or contig is identified as belonging to a gene family, 
>>gene, or protein domain, check within that group for  species identities. 
>>Then you compare apples to apples in terms of gene conservation level
>> 
>>Does anybody know a program that would do this efficiently from metagenomic 
>>data?
>>
>>Gerald Bothe
>>
>>
>>From: Scott W. Tighe mailto:scott.ti...@uvm.edu
>>>To: galaxy-user@lists.bx.psu.edu 
>>>Sent: Wednesday, September 18, 2013 10:03 AM
>>>Subject: Re: [galaxy-user] Metagenomic filtering
>>>
>>>
>>>Dear Galaxy
>>>
>>>When running HiSeq shot metagenomics sample from the environment against 
>>>megablast and taxonomic representation, How do I filter/remove all the 16s 
>>>and other conserved sequences.
>>>
>>>The problem if blasting a single organism that has a fraction of conserved 
>>>sequence, the results will align with E.coli 10,000 times more then the 
>>>possible target organism. This data would be wrong and misleading. For 
>>>example a 100mg sample that was negative for e coli using MUG test, give 
>>>thousands of hits with galaxy.
>>>
>>>1) Is there a "filter conserved sequences" setting?
>>>
>>>
>>>
>>>2) Is there a "remove model organisms" setting?
>>>
>>>
>>>Scott Tighe
>>>--Core Laboratory Research Staff
>>>Advanced Genome Technologies Core
>>>Deep Sequencing (MPS) Facility
>>>Vermont Cancer Center
>>>149 Beaumont Ave
>>>University of Vermont HSRF 303
>>>Burlington Vermont  USA 05045
>>>802-656-AGTC
>>>802-999-6666 (cell)
>>>
>>>
>>>
>>>Quoting Jennifer Jackson <j...@bx.psu.edu>:
>>>
>>>> Hello Elwood,
>>>> 
>>>> Are you still having connection issues today? Or is this resolved?
>>>> 
>>>> Best,
>>>> 
>>>> Jen
>>>> Galaxy team
>>>> 
>>>> On 9/13/13 11:36 AM, Elwood Linney wrote:
>>>>> A message sent earlier this week by me indicated that I could not connect 
>>>>> to Galaxy via Fetch to download data.
>>>>> 
>>>>> A reply indicated a glitch was fixed.
>>>>> 
>>>>> I then could connect with Fetch and I tried to transfer 4 x 16gb files 
>>>>> and the connection disconnected about 4 times.
>>>>> 
>>>>> Now, once again, I cannot connect with Galaxy online to transfer data.
>>>>> 
>>>>> Is this a problem that can be solved-either at my end or at Galaxy?
>>>>> 
>>>>> Elwood Linney
>>>>> 
>>>>> 
>>>>> ___________________________________________________________
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>>>> 
>>>> --Jennifer Hillman-Jackson
>>>> http://galaxyproject.org/
>>>
>>>
>>>
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>
>
>
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