Pakket: augustus (3.5.0+dfsg-4 en anderen) [debports]

[ Bron:  ]

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.

Andere aan augustus gerelateerde pakketten

• 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 Library

• dep: libc6.1 (>= 2.34)

  GNU C Bibliotheek: Gedeelde bibliotheken
  Ook een virtueel pakket geboden door: libc6.1-udeb

• dep: libcolamd3 (>= 1:7.0.1)

  column approximate minimum degree ordering library for sparse matrices

• dep: libgcc-s1 (>= 3.4)

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• 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)

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• dep: libmysql++3t64

  MySQL C++ library bindings (runtime)

• dep: libsqlite3-0 (>= 3.5.9)

  SQLite 3 shared library

• dep: libstdc++6 (>= 14)

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• 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

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• sug: libfile-which-perl

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• sug: python3-biopython

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augustus downloaden

Pakket downloaden voor alle beschikbare platforms

Platform	Versie	Pakketgrootte	Geïnstalleerde grootte	Bestanden
alpha (unofficial port)	3.5.0+dfsg-4+b5	1.897,4 kB	13.079,0 kB	[overzicht]