Paket: augustus (3.5.0+dfsg-4 ve diğerleri)

[ Kaynak: 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.

Etiketler: Alan: Biyoloji, Biyoinformatik, Geliştirildiği dil: implemented-in::c++, interface::commandline, Rol: Program, Bilim: science::calculation, scope::utility, Arayüz Araç Takımı: Ncurses TUI, Amaç: use::analysing, works-with::biological-sequence

augustus ile İlgili Diğer Paketler

• dep: augustus-data

  data files for AUGUSTUS

• dep: libbamtools2.5.1 (>= 2.5.1+dfsg) [ia64]

  Paket mevcut değil

• dep: libbamtools2.5.2 (>= 2.5.2+dfsg) [ia64 değil]

  dynamic library for manipulating BAM (genome alignment) files

• dep: libboost-iostreams1.74.0 (>= 1.74.0) [ia64]

  Boost.Iostreams Library

• dep: libboost-iostreams1.83.0 (>= 1.83.0) [ia64 değil]

  Boost.Iostreams Library

• dep: libc6 (>= 2.37) [sh4]

  GNU C Library: Shared libraries
  ayrıca şunun tarafından sağlanan bir sanal paket libc6-udeb

  dep: libc6 (>= 2.38) [alpha, ia64, sh4 değil]

• dep: libc6.1 (>= 2.32) [ia64]

  GNU C Library: Shared libraries
  ayrıca şunun tarafından sağlanan bir sanal paket libc6.1-udeb

  dep: libc6.1 (>= 2.34) [alpha]

• dep: libcolamd2 (>= 1:4.5.2) [ia64]

  Paket mevcut değil

• dep: libcolamd3 (>= 1:7.0.1) [ia64 değil]

  column approximate minimum degree ordering library for sparse matrices

• dep: libgcc-s1 (>= 3.0) [amd64, s390x, x32]

  GCC support library

  dep: libgcc-s1 (>= 3.4) [alpha, sparc64]

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

  dep: libgcc-s1 (>= 4.2) [ia64, ppc64, ppc64el, sh4]

  dep: libgcc-s1 (>= 4.5) [arm64, mips64el, riscv64]

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

• dep: libgcc-s2 (>= 4.2.1) [m68k]

  GCC support library

• dep: libgcc-s4 (>= 4.1.1) [hppa]

  GCC support library

• dep: libgsl25 (>= 2.6) [ia64]

  Paket mevcut değil

• dep: libgsl28 (>= 2.8+dfsg) [ia64 değil]

  GNU Scientific Library (GSL) -- library package

• dep: libgslcblas0 (>= 2.8) [sparc64]

  GNU Scientific Library (GSL) -- blas library package

• dep: libhts3 (>= 1.10) [ia64]

  C library for high-throughput sequencing data formats

• dep: libhts3t64 (>= 1.17) [ia64 değil]

  C library for high-throughput sequencing data formats

• dep: libmariadb3 (>= 3.0.0)

  MariaDB database client library

• dep: libmysql++3t64 [ia64 değil]

  MySQL C++ library bindings (runtime)

• dep: libmysql++3v5 (>= 3.2.5-1~) [ia64]

  MySQL C++ library bindings (runtime)

• dep: libsqlite3-0 (>= 3.5.9)

  SQLite 3 shared library

• dep: libstdc++6 (>= 13.1) [m68k, sh4]

  GNU Standard C++ Library v3

  dep: libstdc++6 (>= 14) [ia64, m68k, sh4 değil]

  dep: libstdc++6 (>= 9) [ia64]

• dep: libunwind8 [ia64]

  library to determine the call-chain of a program - runtime

• dep: zlib1g (>= 1:1.1.4) [sparc64]

  compression library - runtime

• 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

augustus indir

Tüm mevcut mimariler için indir

Mimari	Sürüm	Paket Boyutu	Kurulu Boyut	Dosyalar
alpha (resmi olmayan port)	3.5.0+dfsg-4+b5	1.897,4 kB	13.079,0 kB	[dosya listesi]
amd64	3.5.0+dfsg-4+b5	2.116,0 kB	11.565,0 kB	[dosya listesi]
arm64	3.5.0+dfsg-4+b5	1.816,6 kB	11.067,0 kB	[dosya listesi]
armel	3.5.0+dfsg-4+b5	1.796,0 kB	10.806,0 kB	[dosya listesi]
armhf	3.5.0+dfsg-4+b5	1.722,3 kB	7.710,0 kB	[dosya listesi]
hppa (resmi olmayan port)	3.5.0+dfsg-4	1.832,3 kB	10.726,0 kB	[dosya listesi]
i386	3.5.0+dfsg-4+b5	2.191,2 kB	12.357,0 kB	[dosya listesi]
ia64 (resmi olmayan port)	3.4.0+dfsg2-3	2.170,0 kB	21.090,0 kB	[dosya listesi]
m68k (resmi olmayan port)	3.5.0+dfsg-4+b4	1.912,3 kB	11.046,0 kB	[dosya listesi]
mips64el	3.5.0+dfsg-4+b5	1.860,1 kB	14.385,0 kB	[dosya listesi]
ppc64 (resmi olmayan port)	3.5.0+dfsg-4	1.991,9 kB	14.650,0 kB	[dosya listesi]
ppc64el	3.5.0+dfsg-4+b5	1.998,1 kB	13.755,0 kB	[dosya listesi]
riscv64	3.5.0+dfsg-4+b6	2.066,9 kB	9.123,0 kB	[dosya listesi]
s390x	3.5.0+dfsg-4+b5	2.013,5 kB	12.262,0 kB	[dosya listesi]
sh4 (resmi olmayan port)	3.5.0+dfsg-4+b4	2.102,5 kB	10.796,0 kB	[dosya listesi]
sparc64 (resmi olmayan port)	3.5.0+dfsg-4	1.681,8 kB	22.589,0 kB	[dosya listesi]
x32 (resmi olmayan port)	3.5.0+dfsg-4+b5	2.133,1 kB	11.143,0 kB	[dosya listesi]