软件包：augustus（3.4.0+dfsg2-3 以及其他的） [debports]
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.
其他与 augustus 有关的软件包
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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 语言运行库：共享库
同时作为一个虚包由这些包填实： libc6-udeb
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- dep: libcolamd2 (>= 1:4.5.2)
- 软件包暂时不可用
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- dep: libgcc-s4 (>= 4.1.1)
- GCC 支持库
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- dep: libgsl27 (>= 2.7.1)
- GNU Scientific Library (GSL) -- library package
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- dep: libhts3 (>= 1.10)
- C library for high-throughput sequencing data formats
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- dep: libmariadb3 (>= 3.0.0)
- MariaDB database client library
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- dep: libmysql++3v5 (>= 3.2.5-1~)
- MySQL C++ library bindings (runtime)
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- dep: libsqlite3-0 (>= 3.5.9)
- SQLite 3 共享库
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- dep: libstdc++6 (>= 11)
- GNU 标准 C++ 库，第3版
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- rec: samtools
- processing sequence alignments in SAM, BAM and CRAM formats
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- sug: cdbfasta
- Constant DataBase indexing and retrieval tools for multi-FASTA files
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- sug: diamond-aligner
- accelerated BLAST compatible local sequence aligner
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- sug: libdbd-mysql-perl
- Perl5 database interface to the MariaDB/MySQL database
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- sug: libfile-which-perl
- Perl module for searching paths for executable programs
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- sug: libparallel-forkmanager-perl
- simple parallel processing fork manager for Perl
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- sug: libyaml-perl
- YAML Ain't Markup Language
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- sug: python3-biopython
- Python3 library for bioinformatics