eLxr packagesパッケージ: augustus (3.5.0+dfsg-2)
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.
その他の augustus 関連パッケージ
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- dep: augustus-data
- data files for AUGUSTUS
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- dep: libbamtools2.5.2 (>= 2.5.2+dfsg)
- dynamic library for manipulating BAM (genome alignment) files
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- dep: libboost-iostreams1.74.0 (>= 1.74.0)
- Boost.Iostreams Library
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- dep: libc6 (>= 2.34)
- GNU C Library: Shared libraries
以下のパッケージによって提供される仮想パッケージでもあります: libc6-udeb
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- dep: libcolamd2 (>= 1:4.5.2)
- column approximate minimum degree ordering library for sparse matrices
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- dep: libgcc-s1 (>= 3.0) [amd64]
- GCC support library
- dep: libgcc-s1 (>= 4.5) [arm64]
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- dep: libgsl27 (>= 2.7.1)
- GNU Scientific Library (GSL) -- library package
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- dep: libhts3 (>= 1.10)
- パッケージは利用できません
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- dep: libmariadb3 (>= 3.0.0)
- MariaDB database client library
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- dep: libmysql++3v5 (>= 3.2.5-1~)
- パッケージは利用できません
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- dep: libsqlite3-0 (>= 3.5.9)
- SQLite 3 shared library
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- dep: libstdc++6 (>= 11)
- GNU Standard C++ Library v3
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- rec: samtools
- パッケージは利用できません
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- sug: cdbfasta
- Constant DataBase indexing and retrieval tools for multi-FASTA files
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- sug: diamond-aligner
- パッケージは利用できません
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- sug: libdbd-mysql-perl
- パッケージは利用できません
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- sug: libfile-which-perl
- Perl module for searching paths for executable programs
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- sug: libparallel-forkmanager-perl
- パッケージは利用できません
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- sug: libyaml-perl
- YAML Ain't Markup Language
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- sug: python3-biopython
- パッケージは利用できません