cpet
/
freebsd-ports
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

biology/barrnap: Update descr

This commit is contained in:
Yuri Victorovich 2022-11-24 19:12:18 -08:00
parent a7eec55e9c
commit 20cc8e440a
1 changed files with 8 additions and 6 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

14
biology/barrnap/pkg-descr
View File

@ -1,6 +1,8 @@
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).
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.