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

[ Source: augustus  ]

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

• 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 (>= 2.38)

  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 (>= 4.5)

  GCC:n apukirjasto

• dep: libgsl28 (>= 2.8+dfsg)

  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 (>= 14)

  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
riscv64	3.5.0+dfsg-4+b6	2,066.9 kt	9,123.0 kt	[tiedostoluettelo]