Barrnap: Bacterial ribosomal RNA predictor
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)....2563 days ago
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Curated set of ribosomal RNA (rRNA) reference sequences (targeted loci) with verifiable organism
...al for correctly identifying and classifying prokaryotic (bacteria and archaea) and fungal samples. To provi...; *16S ribosomal RNA (Bacteria and Archaea) &nb...1546 days ago
Download the genome from NCBI using bash script/command
...d -r 's|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_genomic.fna.gz|' > genomic_file_plant # -for archaea curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/archaea/assembly_summary.txt' | awk '...2545 days ago
Download the gff files from NCBI using bash script/command
...d -r 's|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_genomic.gff.gz|' > genomic_file_plant # -for archaea curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/archaea/assembly_summary.txt' | awk '...2536 days ago
Comment on "Tools to detect synteny blocks regions among multiple genomes"
Useful bacterial gene synteny explorer @ http://archaea.u-psud.fr/synttax/ and http://archaea.u-psud.fr/absynte/2741 days ago