Unified Human Gastrointestinal Proteome clustering results by DPCfam

This dataset contains the result of clustering the Unified Human Gastrointestinal Proteome using the DPCfam algorithm. More details on the DPCfam clustering algorithm can be found in the original publication: Russo, Elena Tea, et al. "DPCfam: Unsupervised protein family classification by Density Peak Clustering of large sequence datasets." PLOS Computational Biology 18.10 (2022): e1010610. https://doi.org/10.1371/journal.pcbi.1010610 All of the putative protein families obtained through DPCfam (including previous results) can be browsed online at our dedicated webserver: https://dpcfam.areasciencepark.it/uhgp The original protein dataset is version 1.0 of the UHGP-50 dataset, available for download from MGnify at https://www.ebi.ac.uk/metagenomics/. FILES DESCRIPTION: Only MCs with seeds with 1) more than 50 elements and 2) average length larger than 50 aminoacids are reported. metaclusters_xml.tar.gz: dpcfam_uhgp_metaclusters.xml: Metaclusters' seeds. Metaclusters entries include also some statistical information about each MC (such as size, average length, low complexity fraction, etc.) and Pfam comparison (Dominant Architecture). dpcfam_metaclusters.xsd: XML schema file for the data. MCxml_to_tables.awk: Awk script to convert from XML to tabular text files. Use through the parse.sh script. parse.sh: XML parser. README.md uhgp_xml.tar.gz: uhgp_proteins.xml: XML file containing all of UHGP-50 proteins and its corresponding sequences, annotated with Pfam and DPCfam metacluster data. Annotations comprise the membership of a protein as a seed or matches found though the profile-hmms of the DPCfam-UHGP and the DPCfam-Uniref clusterings. uhgp_matches.xsd: XML schema file for the data. xml_to_list.awk: Awk script to convert from XML to tabular text files. Use through the parse.sh script. xml_to_list_mcfiles.awk: Awk script to convert from XML to tabular text files (including individual files for metaclusters' seeds). Use through the parse.sh script. parse.sh: XML parser. README.md Metacluster Files: seeds.zip: Metaclusters' seed sequences. A fasta file for each metacluster before filtering. filtered_seeds.zip: Metaclusters' seed sequences after clustering at 60 percent identity. metaclusters_hmms.tar.gz: Metaclusters' profile-hmms. A ".hmm" file for each metacluser. metaclusters_msas.tar.gz: Metaclusters' multiple sequence alignments, in fasta format.

本数据集包含使用DPCfam算法对统一人类肠道蛋白质组（Unified Human Gastrointestinal Proteome, UHGP）进行聚类得到的结果。有关DPCfam聚类算法的更多细节可参阅原始研究论文：Russo, Elena Tea 等人的"DPCfam: Unsupervised protein family classification by Density Peak Clustering of large sequence datasets"，发表于《PLOS Computational Biology》2022年第18卷第10期，论文编号e1010610，DOI: 10.1371/journal.pcbi.1010610。通过DPCfam获得的所有推定蛋白质家族（包括既往研究结果）均可通过专用在线服务器浏览：https://dpcfam.areasciencepark.it/uhgp。原始蛋白质数据集为UHGP-50数据集的1.0版本，可从MGnify平台（https://www.ebi.ac.uk/metagenomics/）下载获取。

## 文件说明
仅收录满足以下两项条件的元簇（Metaclusters, MCs）种子：1）元素数量超过50；2）平均长度大于50个氨基酸。

### metaclusters_xml.tar.gz
- dpcfam_uhgp_metaclusters.xml：元簇的种子信息文件。元簇条目还包含每个元簇（MC）的多项统计信息（如簇大小、平均长度、低复杂度序列占比等）以及Pfam比对结果（主导架构）。
- dpcfam_metaclusters.xsd：该数据集的XML模式文件。
- MCxml_to_tables.awk：用于将XML格式转换为表格文本文件的Awk脚本，需通过parse.sh脚本运行。
- parse.sh：XML解析器。
- README.md

### uhgp_xml.tar.gz
- uhgp_proteins.xml：包含所有UHGP-50蛋白质及其对应序列的XML文件，已标注Pfam和DPCfam元簇相关信息。标注内容涵盖蛋白质作为种子的成员身份，或通过DPCfam-UHGP与DPCfam-UniRef聚类的轮廓隐马尔可夫模型（profile-HMMs）匹配得到的结果。
- uhgp_matches.xsd：该数据集的XML模式文件。
- xml_to_list.awk：用于将XML格式转换为表格文本文件的Awk脚本，需通过parse.sh脚本运行。
- xml_to_list_mcfiles.awk：用于将XML格式转换为表格文本文件的Awk脚本（包含元簇种子的单独输出文件），需通过parse.sh脚本运行。
- parse.sh：XML解析器。
- README.md

### 元簇文件
- seeds.zip：元簇的种子序列压缩包，每个元簇在过滤前对应一个FASTA格式文件。
- filtered_seeds.zip：经过60%序列同一性聚类过滤后的元簇种子序列压缩包。
- metaclusters_hmms.tar.gz：元簇的轮廓隐马尔可夫模型（profile-HMMs）压缩包，每个元簇对应一个".hmm"格式文件。
- metaclusters_msas.tar.gz：元簇的多序列比对文件压缩包，格式为FASTA。