Datasets and codes for repeats annotation in genome

1) Files begin with 'all_retrovirus.' in 'report_run' are data we used to identify retrovirus (see detail in supplementary 1.5.3); 2) Files begin with 'GB_TE.new' in 'GBTE_data' are index files we used to identify reverse transcriptase and TE sequences from NCBI (see detail in supplementary 1.5.3); 3) 'report_run' are codes used to run reportsJ.pl (see detail in supplementary 1.5.3); 4) Files begin with 'sprot.' in 'report_run' are index files we used to identify proteins (see detail in supplementary 1.5.3); 5) 'Vertebrate_use.fa' is Vertebrate repeat consensus sequences downloaded from Repbase, we used it as CENSOR library (see detail in supplementary 1.5.1); 6) 'our_known_reps_20130520' was used in the first CENSOR run (see detail in supplementary 1.5.1). 7) 'RepBase20.04.fasta' used in last step of TE annotation, contains CENSOR TE references

1) `report_run`目录下以`all_retrovirus.`为前缀的文件，为本研究用于鉴定逆转录病毒的数据集（详细说明参见补充材料1.5.3）；2) `GBTE_data`目录下以`GB_TE.new`为前缀的文件，为本研究用于从美国国家生物技术信息中心（National Center for Biotechnology Information，NCBI）中鉴定逆转录酶与转座因子（transposable element, TE）序列的索引文件（详细说明参见补充材料1.5.3）；3) `report_run`为用于执行`reportsJ.pl`的代码集（详细说明参见补充材料1.5.3）；4) `report_run`目录下以`sprot.`为前缀的文件，为本研究用于鉴定蛋白质的索引文件（详细说明参见补充材料1.5.3）；5) `Vertebrate_use.fa`为从Repbase数据库下载的脊椎动物重复序列共有序列，本研究将其用作CENSOR文库（详细说明参见补充材料1.5.1）；6) `our_known_reps_20130520`用于首次CENSOR注释流程（详细说明参见补充材料1.5.1）；7) `RepBase20.04.fasta`用于转座因子注释流程的最后一步，其包含CENSOR转座因子参考序列集