Paket: augustus (3.5.0+dfsg-2)

[ Källkod: 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.

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

Andra paket besläktade med augustus

• 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-iostreams1.74.0 (>= 1.74.0)

  Boost.Iostreams Library

• dep: libc6 (>= 2.34)

  GNU C-bibliotek: Delade bibliotek
  också ett virtuellt paket som tillhandahålls av libc6-udeb

• dep: libcolamd2 (>= 1:4.5.2)

  column approximate minimum degree ordering library for sparse matrices

• dep: libgcc-s1 (>= 3.0) [amd64, s390x]

  GCC stödbibliotek

  dep: libgcc-s1 (>= 3.5) [armel, armhf]

  dep: libgcc-s1 (>= 4.2) [mipsel, ppc64el]

  dep: libgcc-s1 (>= 4.5) [arm64, mips64el]

  dep: libgcc-s1 (>= 7) [i386]

• dep: libgsl27 (>= 2.7.1)

  GNU Scientific Library (GSL) -- library package

• dep: libhts3 (>= 1.10)

  C library for high-throughput sequencing data formats

• dep: libmariadb3 (>= 3.0.0)

  MariaDB database client library

• dep: libmysql++3v5 (>= 3.2.5-1~)

  MySQL C++ library bindings (runtime)

• dep: libsqlite3-0 (>= 3.5.9)

  SQLite 3 shared library

• dep: libstdc++6 (>= 11)

  GNU standardbibliotek v3 för C++

• 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

Hämta augustus

Hämtningar för alla tillgängliga arkitekturer

Arkitektur	Paketstorlek	Installerad storlek	Filer
amd64	2.000,1 kbyte	10.856,0 kbyte	[filförteckning]
arm64	1.715,1 kbyte	10.617,0 kbyte	[filförteckning]
armel	1.693,3 kbyte	10.781,0 kbyte	[filförteckning]
armhf	1.631,3 kbyte	7.837,0 kbyte	[filförteckning]
i386	2.074,9 kbyte	11.756,0 kbyte	[filförteckning]
mips64el	1.817,8 kbyte	14.215,0 kbyte	[filförteckning]
mipsel	1.835,9 kbyte	13.506,0 kbyte	[filförteckning]
ppc64el	1.934,1 kbyte	13.434,0 kbyte	[filförteckning]
s390x	1.755,7 kbyte	11.409,0 kbyte	[filförteckning]