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SIMD-vectorized implementation of the Viterbi algorithm for profile HMM | ||
alignment and introduced various other speed-ups. This accelerated HHsearch by a | ||
factor 4 and HHblits by a factor 2 over the previous version 2.0.16. HHblits3 is | ||
~10x faster than PSI-BLAST and ~20x faster than HMMER3. Jobs to perform HHsearch | ||
and HHblits searches with many query profile HMMs can be parallelized over cores | ||
and over servers in a cluster using OpenMP and message passing interface (MPI). | ||
Barrnap predicts the location of ribosomal RNA genes in genomes. It supports | ||
bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), metazoan mitochondria | ||
(12S,16S) and eukaryotes (5S,5.8S,28S,18S). | ||
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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. | ||
Multithreading is supported and one can expect roughly linear speed-ups with | ||
more CPUs. |