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Re: Licensing terms for data derived from ARB/SILVA data

Dear Sascha Steinbiss,
thanks for the information.
We discussed it and in general we agree that the HMM profiles derived from LSURef_115_tax_silva_full_align_trunc.fasta can be distributed. But we would like to ask you to clearly indicate that the profiles are only free for non-commercial usage, commercial users need a licence. The easiest approach is to add a reference to the SILVA terms of license assigned to the software/profile.

Have a nice weekend

Frank Oliver Glöckner

Am 26.11.2014 20:28, schrieb Sascha Steinbiss:
On 26/11/2014 17:56, Frank Oliver Glöckner wrote:
>Dear Sascha Steinbeiss,
Dear Prof. Gloeckner,

thanks for your prompt reply.

>Before we can answer your question may I ask you to provide us with some
>more information about the:
>1. name of the tool
The software in question is barrnap
(http://www.vicbioinformatics.com/software.barrnap.shtml) written by
Torsten Seemann.

>2. functionality of the tool, e.g. does it just detect rRNAs, and/or
>does it classify sequences?
The main functionality is to detect rRNAs and to output their locations
in an input sequence as GFF3 features. As far as classification goes, it
does distinguish between the individual rRNAs for a given kingdom
(5S,23S,16S for bacteria; 5S,5.8S,28S,18S for eukaryotes, etc.) but does
not taxonomically classify them as being close to a particular
species. You can see example output on the web page given above.

It is basically a wrapper around nhmmer searching for a relatively
general rRNA pHMM, meant for de novo annotation.

>All  the best
>Frank Oliver Glöckner
Best wishes from a former 'Nordlicht' (I think we met once when I still
was at the ZBH Hamburg)
Sascha Steinbiss

>Am 26.11.2014 12:34, schrieb Sascha Steinbiss:
>>Dear ARB/SILVA team,
>>I am writing to inquire about a special case regarding your data
>>licensing terms.
>>I am involved with the Debian Med project
>>(https://www.debian.org/devel/debian-med/), whose goal it is to provide
>>software from the medical and bioinformatics fields to users of the
>>Debian Linux distribution. Currently I am working on packaging a piece
>>of free (GPL) software for prediction of rRNA genes in sequences. This
>>software requires (and would be bundled with) a set of nucleotide
>>profile HMMs (built with HMMER) based on several individual data
>>sources. One of the data sources used to build these HMMs was the file
>>LSURef_115_tax_silva_full_align_trunc.fasta, available from your
>>Since your licensing terms
>>(http://www.arb-silva.de/silva-license-information/) are not clear about
>>how derivatives of your data are to be licensed, I would like to ask
>>whether it would be OK for us to package and redistribute these HMMs
>>under a free license, for both academic and non-academic users. I wish
>>to make it clear here that the original file
>>LSURef_115_tax_silva_full_align_trunc.fasta will NOT be included in the
>>package, only HMMs built from it (and other free sources).
>>I am looking forward to your response.
>>Best regards
>>Sascha Steinbiss

Prof. Dr. Frank Oliver Glöckner
Head of the Microbial Genomics and Bioinformatics Research Group
Max Planck Institute for Marine Microbiology
Jacobs University Bremen gGmbH

E-mail: fog@mpi-bremen.de

MPI for Marine Microbiology
Celsiusstrasse 1
28359 Bremen

MPI:    +49 (0) 421 2028 970
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