Plastid sequences about pr2database

[vaulot]

Hi

Sorry for the confusion, but at present the plastid 16S rRNA sequences are not included in the PR2. We are planning to include the whole PhytoRef into PR2 at a latter date . So at present no dereplication needed. Cheers. Daniel

[rspreafico-sgi]

Thank you for the fast reply and for amending the readme file. Would this sentence in the readme file also require amendments?

The database mainly consists of nuclear-encoded protistan sequences. However, metazoans, land plants, macrosporic fungi and eukaryotic organelles (mitochondrion, plastid and others) are also included because they are useful for the analysis of high-troughput sequencing data sets.

I will download the plastid sequences from PhytoREF. Do you have a recommended source for mitochondrial rRNA sequences, or maybe a section of early releases of PR2 when they still included mitochondrial sequences?

[vaulot]

Thank you for the fast reply and for amending the readme file. Would this sentence in the readme file also require amendments?

The database mainly consists of nuclear-encoded protistan sequences. However, metazoans, land plants, macrosporic fungi and eukaryotic organelles (mitochondrion, plastid and others) are also included because they are useful for the analysis of high-troughput sequencing data sets.

Yes absolutely, done now.

I will download the plastid sequences from PhytoREF. Do you have a recommended source for mitochondrial rRNA sequences, or maybe a section of early releases of PR2 when they still included mitochondrial sequences?

No unfortunately I do not have a suggestion. Probably you could use the Silva database. On the PR2 side, I will try to do some archaeology but unfortunately the PR2 server is long gone and had never been mirrored. I will get back to you if I find anything and if I do not, will add this on my to do list.

Thanks a lot for your feedback.

[rspreafico]

Thank you for looking into this!