biology/tRNAscan-SE 2.0.11 FreeBSD

Searching for tRNA genes in genomic sequence

System: FreeBSD
Repository: FreeBSD ports
Maintainer: [email protected]
License: GPLv3+
Categories: biology

Description

tRNAscan-SE was written in the PERL (version 5.0) script language. Input consists of DNA or RNA sequences in FASTA format. tRNA predictions are output in standard tabular or ACeDB format. tRNAscan-SE does no tRNA detection itself, but instead combines the strengths of three independent tRNA prediction programs by negotiating the flow of information between them, performing a limited amount of post-processing, and outputting the results in one of several formats.

In the other systems

System

Port

Version

FreeBSD

biology/tRNAscan-SE

2.0.11

DragonFly

biology/tRNAscan-SE

2.0.11

GhostBSD

biology/tRNAscan-SE

2.0.11

Install

Binary package:

pkg install tRNAscan-SE

From the ports tree:

cd /usr/ports/biology/tRNAscan-SE/ && make install clean

To depend on this port in another port's Makefile:

RUN_DEPENDS=	tRNAscan-SE>0:biology/tRNAscan-SE

Packages

The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.

Repository	aarch64	amd64	armv6	armv7	i386
FreeBSD:14:latest	-	2.0.11	-	-	2.0.11
FreeBSD:14:quarterly	-	2.0.11	n/a	-	2.0.11
FreeBSD:15:latest	-	2.0.11	n/a	-	2.0.11
FreeBSD:15:quarterly	-	2.0.11	n/a	n/a	n/a
FreeBSD:16:latest	-	2.0.11	n/a	n/a	n/a
FreeBSD:16:quarterly	n/a	n/a	n/a	n/a	n/a

Dependencies

As this port's Makefile names them.

Runtime 1

cmsearch : biology/infernal

The full lists below include those, and their dependencies in turn.

Build dependencies 7

Run dependencies 2

No port depends on this one.

Configuration

No options to configure.

USES: autoreconf perl5
Service scripts: none

Files

pkg-plist 140

bin/EukHighConfidenceFilter
bin/MitoHighConfidenceFilter
bin/covels-SE
bin/coves-SE
bin/eufindtRNA
bin/fasta2gsi
bin/sstofa
bin/tRNAscan-SE
bin/trnascan-1.4
etc/tRNAscan-SE.conf
share/tRNAscan-SE/gcode/gcode.cilnuc
share/tRNAscan-SE/gcode/gcode.echdmito
share/tRNAscan-SE/gcode/gcode.invmito
share/tRNAscan-SE/gcode/gcode.marsumito
share/tRNAscan-SE/gcode/gcode.othmito
share/tRNAscan-SE/gcode/gcode.vertmito
share/tRNAscan-SE/gcode/gcode.ystmito
share/tRNAscan-SE/models/Cren-eury-BHB-noncan.cm
share/tRNAscan-SE/models/Dsignal
share/tRNAscan-SE/models/ESELC.cm
share/tRNAscan-SE/models/PSELC.cm
share/tRNAscan-SE/models/TPCsignal
share/tRNAscan-SE/models/TRNA2-arch.cm
share/tRNAscan-SE/models/TRNA2-archns.cm
share/tRNAscan-SE/models/TRNA2-bact.cm
share/tRNAscan-SE/models/TRNA2-bactns.cm
share/tRNAscan-SE/models/TRNA2-euk.cm
share/tRNAscan-SE/models/TRNA2-eukns.cm
share/tRNAscan-SE/models/TRNA2.cm
share/tRNAscan-SE/models/TRNA2ns.cm
share/tRNAscan-SE/models/TRNAinf-1415-ns.cm
share/tRNAscan-SE/models/TRNAinf-1415.cm
share/tRNAscan-SE/models/TRNAinf-arch-3h.cm
share/tRNAscan-SE/models/TRNAinf-arch-5h.cm
share/tRNAscan-SE/models/TRNAinf-arch-SeC.cm
share/tRNAscan-SE/models/TRNAinf-arch-iso
share/tRNAscan-SE/models/TRNAinf-arch-iso.i1f
share/tRNAscan-SE/models/TRNAinf-arch-iso.i1i
share/tRNAscan-SE/models/TRNAinf-arch-iso.i1m
share/tRNAscan-SE/models/TRNAinf-arch-iso.i1p
share/tRNAscan-SE/models/TRNAinf-arch-ns.cm
share/tRNAscan-SE/models/TRNAinf-arch.cm
share/tRNAscan-SE/models/TRNAinf-bact-SeC.cm
share/tRNAscan-SE/models/TRNAinf-bact-iso
share/tRNAscan-SE/models/TRNAinf-bact-iso.i1f
share/tRNAscan-SE/models/TRNAinf-bact-iso.i1i
share/tRNAscan-SE/models/TRNAinf-bact-iso.i1m
share/tRNAscan-SE/models/TRNAinf-bact-iso.i1p
share/tRNAscan-SE/models/TRNAinf-bact-ns.cm
share/tRNAscan-SE/models/TRNAinf-bact.cm
share/tRNAscan-SE/models/TRNAinf-euk-SeC.cm
share/tRNAscan-SE/models/TRNAinf-euk-iso
share/tRNAscan-SE/models/TRNAinf-euk-iso.i1f
share/tRNAscan-SE/models/TRNAinf-euk-iso.i1i
share/tRNAscan-SE/models/TRNAinf-euk-iso.i1m
share/tRNAscan-SE/models/TRNAinf-euk-iso.i1p
share/tRNAscan-SE/models/TRNAinf-euk-ns.cm
share/tRNAscan-SE/models/TRNAinf-euk.cm
share/tRNAscan-SE/models/TRNAinf-mito-mammal
share/tRNAscan-SE/models/TRNAinf-mito-mammal-Ala.cm
share/tRNAscan-SE/models/TRNAinf-mito-mammal-Arg.cm
share/tRNAscan-SE/models/TRNAinf-mito-mammal-Asn.cm
share/tRNAscan-SE/models/TRNAinf-mito-mammal-Asp.cm
share/tRNAscan-SE/models/TRNAinf-mito-mammal-Cys.cm
share/tRNAscan-SE/models/TRNAinf-mito-mammal-Gln.cm
share/tRNAscan-SE/models/TRNAinf-mito-mammal-Glu.cm
share/tRNAscan-SE/models/TRNAinf-mito-mammal-Gly.cm
share/tRNAscan-SE/models/TRNAinf-mito-mammal-His.cm
share/tRNAscan-SE/models/TRNAinf-mito-mammal-Ile.cm
share/tRNAscan-SE/models/TRNAinf-mito-mammal-LeuTAA.cm
share/tRNAscan-SE/models/TRNAinf-mito-mammal-LeuTAG.cm
share/tRNAscan-SE/models/TRNAinf-mito-mammal-Lys.cm
share/tRNAscan-SE/models/TRNAinf-mito-mammal-Met.cm
share/tRNAscan-SE/models/TRNAinf-mito-mammal-Phe.cm
share/tRNAscan-SE/models/TRNAinf-mito-mammal-Pro.cm
share/tRNAscan-SE/models/TRNAinf-mito-mammal-SerGCT.cm
share/tRNAscan-SE/models/TRNAinf-mito-mammal-SerTGA.cm
share/tRNAscan-SE/models/TRNAinf-mito-mammal-Thr.cm
share/tRNAscan-SE/models/TRNAinf-mito-mammal-Trp.cm
share/tRNAscan-SE/models/TRNAinf-mito-mammal-Tyr.cm
share/tRNAscan-SE/models/TRNAinf-mito-mammal-Val.cm
share/tRNAscan-SE/models/TRNAinf-mito-mammal.i1f
share/tRNAscan-SE/models/TRNAinf-mito-mammal.i1i
share/tRNAscan-SE/models/TRNAinf-mito-mammal.i1m
share/tRNAscan-SE/models/TRNAinf-mito-mammal.i1p
share/tRNAscan-SE/models/TRNAinf-mito-vert
share/tRNAscan-SE/models/TRNAinf-mito-vert-Ala.cm
share/tRNAscan-SE/models/TRNAinf-mito-vert-Arg.cm
share/tRNAscan-SE/models/TRNAinf-mito-vert-Asn.cm
share/tRNAscan-SE/models/TRNAinf-mito-vert-Asp.cm
share/tRNAscan-SE/models/TRNAinf-mito-vert-Cys-no-darm.cm
share/tRNAscan-SE/models/TRNAinf-mito-vert-Cys.cm
share/tRNAscan-SE/models/TRNAinf-mito-vert-Gln.cm
share/tRNAscan-SE/models/TRNAinf-mito-vert-Glu.cm
share/tRNAscan-SE/models/TRNAinf-mito-vert-Gly.cm
share/tRNAscan-SE/models/TRNAinf-mito-vert-His.cm
share/tRNAscan-SE/models/TRNAinf-mito-vert-Ile.cm
share/tRNAscan-SE/models/TRNAinf-mito-vert-LeuTAA.cm
share/tRNAscan-SE/models/TRNAinf-mito-vert-LeuTAG.cm
share/tRNAscan-SE/models/TRNAinf-mito-vert-Lys.cm

The first 100 are listed.

distinfo 1

File

Size

SHA256

trnascan-se-2.0.11.tar.gz

4.430973e+06

29b74edd0f84ad88139035e119b66397c54a37428e0b61c66a1b3d4733adcd1e

Master sites 1

http://trna.ucsc.edu/software/

Commit history 0

No commits in the history this site was built from.