Dfam: sustainable growth, curation support, and improved quality for mobile element annotation

项目总结/摘要 重复DNA，特别是由于转座因子（TE），构成了许多基因组的很大一部分。 基因组中重复内容的彻底和准确的注释依赖于一个全面的数据库， 已知的TE，沿着的是用于识别元素的衰变实例的稳健的统计和程序方法 理清他们复杂的关系 TE实例的注释通常使用我们的RepeatMasker软件进行，该软件比较基因组 到包含已知重复家族的表示的数据库。这些在历史上是共识 序列，其通常近似于原始TE的序列。我们的Dfam数据库是一个开放的 访问重复DNA家族的集合，其中每个家族由多个序列表示 比对和轮廓隐马尔可夫模型（HMM）。我们已经证明了配置文件HSPER支持 提高注释灵敏度，Dfam为TE家庭的策展人和那些 使用产生的注释。 在此期间，该数据库已发展到包括属于1000多个物种的家庭 (from基线为5）。这种增长带来了一些基于规模的压力，在某些情况下， 迫使我们减少Dfam的功能作为回应，在其他情况下， 能更好地满足社会的需要。我们建议的工作主要针对这些问题，同时继续 扩大和多样化资源。

Project Summary / Abstract Repetitive DNA, especially that due to transposable elements (TEs), makes up a large fraction of many genomes. Thorough and accurate annotation of repetitive content in genomes depends on a comprehensive database of known TEs, along with robust statistical and procedural methods for recognizing decayed instances of elements and disentangling their complex relationships. Annotation of TE instances is usually performed using our RepeatMasker software, which compares a genome to a database containing representations of known repeat families. These have historically been consensus sequences, which generally approximate the sequences of the original TEs. Our Dfam database is an open access collection of repetitive DNA families, in which each family is represented by a multiple sequence alignment and a profile hidden Markov model (HMM). We have demonstrated that profile HMMs support improved annotation sensitivity, and Dfam provides numerous aids to both curators of TE families and those who make use of the resulting annotations. During the life of this grant, the database has grown to include families belonging to more than 1000 species (from a baseline of 5). This growth has introduced a number of scale-based pressures, which in some cases have forced us to reduce Dfam functionality in response, and in other cases highlighted ways that the resource can better meet the needs of the community. Our proposed efforts largely target these matters while continuing to expand and diversify the resource.