Package: augustus (3.3.2 dfsg-2)

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Homepage [bioinf.uni-greifswald.de]

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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.

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

Other Packages Related to augustus

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suggests

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dep: augustus-data

data files for AUGUSTUS
dep: libbamtools2.5.1

dynamic library for manipulating BAM (genome alignment) files
dep: libbz2-1.0

high-quality block-sorting file compressor library - runtime
dep: libc6 (>= 2.15) [not arm64]

GNU C Library: Shared libraries
also a virtual package provided by libc6-udeb

dep: libc6 (>= 2.17) [arm64]
dep: libcurl3-nss (>= 7.23.1)

easy-to-use client-side URL transfer library (NSS flavour)
dep: libgcc1 (>= 1:3.0) [amd64]

GCC support library

dep: libgcc1 (>= 1:3.5) [armhf]

dep: libgcc1 (>= 1:4.5) [arm64]
dep: libhts2 (>= 1.0)

C library for high-throughput sequencing data formats
dep: liblzma5 (>= 5.1.1alpha 20110809)

XZ-format compression library
dep: libncurses6 (>= 6)

shared libraries for terminal handling
dep: libssl1.1 (>= 1.1.0)

Secure Sockets Layer toolkit - shared libraries
dep: libstdc 6 (>= 6)

GNU Standard C Library v3
dep: libtinfo6 (>= 6)

shared low-level terminfo library for terminal handling
dep: zlib1g (>= 1:1.2.3.3)

compression library - runtime

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Download for all available architectures
Architecture	Package Size	Installed Size	Files
amd64	1,134.7 kB	4,787.0 kB	[list of files]
arm64	992.1 kB	4,349.0 kB	[list of files]
armhf	952.2 kB	3,255.0 kB	[list of files]