On 11/28/2014 04:48 PM, Frank Oliver Glöckner wrote: > 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. Argghh! this will prevent from being in free section. And I suppose those profiles are mandary for software usage ?
> > 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 >>>> >>database. >>>> >>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 > > > -- > gpg key id: 4096R/326D8438 (keyring.debian.org) > Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". Trouble? Contact [email protected] Archive: https://lists.debian.org/[email protected]
