ANNOgesic 1.0.6

关于注释性

annogesic是基于rna序列的瑞士军刀 细菌/古细菌基因组。

它是一个模块化的命令行工具，可以集成不同的类型 基于drna-seq（差异rna-seq）或rna-seq的rna-seq数据 包含转录片段以生成高 质量基因组注释。它可以检测基因，cdss/trnas/rrnas， 转录起始位点（TSS）和处理位点，转录， 终止子、未翻译区（UTR）和小RNA（SRNA）； 小型开放阅读框（SORF）、圆形RNA、CRISPR相关RNA， 核糖开关和核糖核酸温度计。它还可以执行rna-rna和 蛋白质-蛋白质相互作用预测。此外，它还将基因分组 进入操纵子和子操纵子并揭示启动子基序。它也可以 将go-term和亚细胞定位分配给基因。几个 annogesic特性是新的实现，而其他构建在 为其提供自适应的已知第三方工具 参数优化。此外，大量的可视化和 统计信息帮助用户快速评估功能预测 由注释性分析得出。工具经过了严格的测试 来自细菌和古细菌的rna序列数据集 样品。

文档

文档可以在 here。

安装

$ pip3 install ANNOgesic

$ pip3 install --user ANNOgesic

$ git clone https://github.com/Sung-Huan/ANNOgesic.git

$ git clone git@github.com:Sung-Huan/ANNOgesic.git

$ cd ANNOgesic/bin
$ ln -s ../annogesiclib .

参数

usage: annogesic [-h] [--version]
                 {create,get_input_files,update_genome_fasta,annotation_transfer,
                  tss_ps,optimize_tss_ps,terminator,transcript,utr,srna,sorf,
                  promoter,operon,circrna,go_term,srna_target,snp,ppi_network,
                  localization,riboswitch_thermometer,crispr,merge_features,
                  screenshot,colorize_screenshot_tracks}
                 ...

positional arguments:
  {create,get_input_files,update_genome_fasta,annotation_transfer,tss_ps,
   optimize_tss_ps,terminator,transcript,utr,srna,sorf,promoter,operon,circrna,
   go_term,srna_target,snp,ppi_network,localization,riboswitch_thermometer,
   crispr,merge_features,screenshot,colorize_screenshot_tracks}
                        commands
    create              Create a project
    get_input_files     Get required files. (i.e. annotation files, fasta
                        files)
    update_genome_fasta
                        Get fasta files of query genomes if the query
                        sequences do not exist.
    annotation_transfer
                        Transfer the annotations from a closely related
                        species genome to a target genome.
    tss_ps              Detect TSSs or processing sites.
    optimize_tss_ps     Optimize TSSs or processing sites based on manual
                        detected ones.
    terminator          Detect rho-independent terminators.
    transcript          Detect transcripts based on coverage file.
    utr                 Detect 5'UTRs and 3'UTRs.
    srna                Detect intergenic, antisense and UTR-derived sRNAs.
    sorf                Detect expressed sORFs.
    promoter            Discover promoter motifs.
    operon              Detect operons and sub-operons.
    circrna             Detect circular RNAs.
    go_term             Extract GO terms from Uniprot.
    srna_target         Detect sRNA-mRNA interactions.
    snp                 Detect SNP/mutation and generate fasta file if
                        mutations were found.
    ppi_network         Detect protein-protein interactions suported by
                        literature.
    localization        Predict subcellular localization of proteins.
    riboswitch_thermometer
                        Predict riboswitches and RNA thermometers.
    crispr              Predict CRISPR related RNAs.
    merge_features      Merge all features to one gff file.
    screenshot          Generate screenshots for selected features using IGV.
    colorize_screenshot_tracks
                        Add color information to screenshots (e.g. useful for
                        dRNA-Seq based TSS and PS detection. It only works
                        after running "screenshot" (after running batch
                        script).

optional arguments:
  -h, --help            show this help message and exit
  --version, -v         show version

引文

许宇，J.沃格尔，库弗斯特纳。2018年，GigaScience， DOI:10.1093/gigascience/giy096， PMID:30169674。

许可证

ISC（互联网系统 联合体许可证~简化的bsd许可证）-请参见LICENSE

联系人

如果您有任何问题，请联系Sung-Huan Yu