Description
SILVA provides comprehensive, quality checked and regularly updated databases of aligned small (16S / 18S, SSU) and large subunit (23S / 28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya). Mac OS X:/Applications/Blast; Windows: C: Blast. 2 Extract the archives of BLAST. Copy the blast installation file for your platform from the aqp-tutorial-files blast-install directory to the directory you've made. In Unix or Linux, extract the files by using the command tar zxvf filename. On Mac OS X or Windows, double-click the file. Less than 25 years ago, the archaea were virtually unknown. We now recognize that these organisms represent one of the fundamental domains of life (32) and constitute a significant fraction of the total biomass (9). Acceptance of the distinct status of the archaea has been largely due to. Centrifuge-download -o taxonomy taxonomy centrifuge-download -o library -m -d 'archaea,bacteria,viral' refseq seqid2taxid.map. To build the index, first concatenate all downloaded sequences into a single file, and then run centrifuge-build.
barrnap website
Barrnap predicts the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S).
It takes FASTA DNA sequence as input, and write GFF3 as output. It uses the new NHMMER tool that comes with HMMER 3.1 for HMM searching in RNA:DNA style. NHMMER binaries for 64-bit Linux and Mac OS X are included and will be auto-detected. Multithreading is supported and one can expect roughly linear speed-ups with more CPUs. Running time is approximately 1 second per 1 megabase of input sequence.
Required Modules
Save the tree by clicking first in the box where the tree is displayed and then press CTRL+P. The saved tree is in postscript format. For Mac users, clicking on the file will convert it automatically to a PDF file. PC users need to use the link provided in the webpage to convert the file to a PDF (PSDPDF).
Serial
- barrnap
System Variables
- HPC_BARRNAP_DIR - installation directory