Paketti: augustus (3.5.0+dfsg-4 ja muut)

Links for augustus

Debian-palvelut:

Imuroi lähdekoodipaketti augustus:

Ylläpitäjät:

External Resources:

Kotisivu [bioinf.uni-greifswald.de]

Samankaltaisia paketteja:

gene prediction in eukaryotic genomes

AUGUSTUS is a software for gene prediction in eukaryotic genomic sequences that is based on a generalized hidden Markov model (HMM), a probabilistic model of a sequence and its gene structure. After learning gene structures from a reference annotation, AUGUSTUS uses the HMM to recognize genes in a new sequence and annotates it with the regions of identified genes. External hints, e.g. from RNA sequencing, EST or protein alignments etc. can be used to guide and improve the gene finding process. The result is the set of most likely gene structures that comply with all given user constraints, if such gene structures exist. AUGUSTUS already includes prebuilt HMMs for many species, as well as scripts to train custom models using annotated genomes.

Tagit: Field: Biology, Bioinformatics, Implemented in: implemented-in::c++, interface::commandline, Role: Program, Tiede: science::calculation, scope::utility, Interface Toolkit: Ncurses TUI, Purpose: use::analysing, works-with::biological-sequence

Muut pakettiin augustus liittyvät paketit

depends

recommends

suggests

enhances

dep: augustus-data

data files for AUGUSTUS
dep: libbamtools2.5.2 (>= 2.5.2+dfsg)

dynamic library for manipulating BAM (genome alignment) files
dep: libboost-iostreams1.83.0 (>= 1.83.0)

Boost.Iostreams -kirjasto
dep: libc6 (>= 2.34)

GNU-C-kirjasto: jaetut kirjastot
myös näennäispaketti, jonka toteuttaa libc6-udeb
dep: libcolamd3 (>= 1:7.0.1)

column approximate minimum degree ordering library for sparse matrices
dep: libgcc-s1 (>= 3.0)

GCC:n apukirjasto
dep: libgsl27 (>= 2.7.1)

GNU Scientific Library (GSL) -- library package
dep: libhts3t64 (>= 1.17)

C library for high-throughput sequencing data formats
dep: libmariadb3 (>= 3.0.0)

MariaDB database client library
dep: libmysql++3t64

MySQL C++ library bindings (runtime)
dep: libsqlite3-0 (>= 3.5.9)

SQLite 3 (jaettu kirjasto)
dep: libstdc++6 (>= 13.1)

GNU standardi C++ -kirjasto, versio 3

rec: samtools

processing sequence alignments in SAM, BAM and CRAM formats

sug: cdbfasta

Constant DataBase indexing and retrieval tools for multi-FASTA files
sug: diamond-aligner

accelerated BLAST compatible local sequence aligner
sug: libdbd-mysql-perl

Perl5 database interface to the MariaDB/MySQL database
sug: libfile-which-perl

Perl module for searching paths for executable programs
sug: libparallel-forkmanager-perl

simple parallel processing fork manager for Perl
sug: libyaml-perl

YAML Ain't Markup Language
sug: python3-biopython

Python3 library for bioinformatics

Imuroi augustus

Imurointi kaikille saataville arkkitehtuureille
Arkkitehtuuri	Versio	Paketin koko	Koko asennettuna	Tiedostot
amd64	3.5.0+dfsg-4+b4	2,043.8 kt	11,117.0 kt	[tiedostoluettelo]