This question seems very basic and I’m not sure if this is the appropriate forum for it–my apologies in advance! I did work involving 16S rRNA sequencing data that I used the mothur MiSeq SOP to analyze. I used the silva.bacteria.fasta file to align my sequences. Is there a version number for the silva database that I can reference? I don’t see a version number on the MiSeq SOP page with the link to download the silva set. I downloaded the silva.bacteria.fasta file in February 2015, if that is useful. Thanks for any help!
This page lists the various versions of the mothur compatible SILVA alignments. Looking at the README’s for each you can see when they were released which may help you with identifying which you were using.
Thank you, Richard! It appears that the release dates for v119 and v123 may be near the top of each of their respective READMEs. Any idea if I am correct in interpreting this? Sorry this is such a naive question…
##From v119 README
wget -N http://www.arb-silva.de/fileadmin/arb_web_db/release_119/ARB_files/SSURef_NR99_119_SILVA_14_07_14_opt.arb.tgz
tar xvzf *arb.tgz
##From v123 README
wget -N http://www.arb-silva.de/fileadmin/arb_web_db/release_123/ARB_files/SSURef_NR99_123_SILVA_12_07_15_opt.arb.tgz
tar xvzf *arb.tgz
I believe those dates are associated with the arb release of the SILVA databases. The mothur compatible databases (the creation of which are documented in the README) were created after. I believe the best date to work from would be the date that the README was posted as the mothur compatible database was likely not released before that… Someone closer to the project can correct me here if I am wrong.
Correct the dates are the dates that SILVA released the databases. If you follow the link that Richard provided, you’ll see the mothur-compatible versions for v 119 and 123.
Is it possible to generate the .fasta format of the silva 123 without having arb software ?
They’re all fasta formatted files. If you want an unaligned set of sequences you can run degap.seqs on the alignment.