Balík: augustus (3.5.0+dfsg-2)

[ Zdroj: 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.

Značky: Pole: Biológia, Bioinformatika, Implementované v: implemented-in::c++, interface::commandline, Role: Program, Veda: science::calculation, scope::utility, Sada nástrojov používateľského rozhrania: Ncurses TUI, Purpose: use::analysing, works-with::biological-sequence

Ostatné balíky súvisiace s balíkom 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)

  knižnica Boost.Iostreams

• dep: libc6 (>= 2.34)

  knižnica GNU C - zdieľané knižnice
  tiež virtuálny balík poskytovaný balíkom libc6-udeb

• dep: libcolamd2 (>= 1:4.5.2)

  knižnica na stĺpcovo približný minimálny stupeň usporiadania riedkych matíc

• dep: libgcc-s1 (>= 3.0)

  podporná knižnica GCC

• dep: libgsl27 (>= 2.7.1)

  GNU Scientific Library (GSL) - balík knižnice

• dep: libhts3 (>= 1.10)

  C library for high-throughput sequencing data formats

• dep: libmariadb3 (>= 3.0.0)

  databáza MariaDB - klientská knižnica

• dep: libmysql++3v5 (>= 3.2.5-1~)

  MySQL C++ library bindings (runtime)

• dep: libsqlite3-0 (>= 3.5.9)

  zdieľaná knižnica SQLite 3

• dep: libstdc++6 (>= 11)

  štandardná knižnica C++ GNU v3

• 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

  rozhranie databáz MariaDB/MySQL pre jazyk Perl 5

• sug: libfile-which-perl

  modul Perlu na nájdenie ciest k spustiteľným programom

• sug: libparallel-forkmanager-perl

  jednoduchý správca forkov na paralelné spracovanie pre jazyk Perl

• sug: libyaml-perl

  YAML Ain't Markup Language

• sug: python3-biopython

  Python3 library for bioinformatics

Stiahnuť augustus

Stiahnuť pre všetky dostupné architektúry

Architektúra	Veľkosť balíka	Nainštalovaná veľkosť	Súbory
amd64	2,000.1 kB	10,856.0 kB	[zoznam súborov]