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Fri, 25 Nov 2022 03:12:37 GMT (envelope-from git) Date: Fri, 25 Nov 2022 03:12:37 GMT Message-Id: <202211250312.2AP3Cbf2047960@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Yuri Victorovich Subject: git: 20cc8e440a21 - main - biology/barrnap: Update descr List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-main@freebsd.org X-BeenThere: dev-commits-ports-main@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: yuri X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 20cc8e440a21cd4ea800573e7fc1edeebc49444d Auto-Submitted: auto-generated X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=20cc8e440a21cd4ea800573e7fc1edeebc49444d commit 20cc8e440a21cd4ea800573e7fc1edeebc49444d Author: Yuri Victorovich AuthorDate: 2022-11-25 03:12:18 +0000 Commit: Yuri Victorovich CommitDate: 2022-11-25 03:12:18 +0000 biology/barrnap: Update descr --- biology/barrnap/pkg-descr | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/biology/barrnap/pkg-descr b/biology/barrnap/pkg-descr index bec4ff368560..7ba80681fff3 100644 --- a/biology/barrnap/pkg-descr +++ b/biology/barrnap/pkg-descr @@ -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.