早期终止转录本与缺失蛋白反映细菌蛋白质组中的假象
Early terminated transcripts and missing proteins reflect artifacts in bacterial proteomes
利用 MMseqs2 聚类与后续过滤，可从细菌蛋白质组中构建覆盖 95% 聚类细菌的核心蛋白集，这些聚类通常涵盖细菌中超过 80% 的蛋白。核心聚类长度高度均一，中位聚类的蛋白有超过 99% 处于众数长度，因此过短（低于众数长度）或过长（超过众数长度 133%）的蛋白很可能是假象。多数“离群”蛋白出现在不到 10% 的聚类中，而“高离群”聚类集中出现在少数蛋白质组里，这些蛋白质组的 BUSCO 片段评分往往较差。短离群蛋白属于假象，至少 80% 的短离群基因组含有该蛋白的众数长度拷贝，只是因移码、终止密码子或起始密码子选择而未被识别。
来源：NAR Genomics and Bioinformatics · doi.org
The high redundancy of many bacterial proteomes can be used to evaluate proteome quality and identify sequence errors. We have used MMseqs2 clustering with subsequent filtering to identify clusters that contain sequences from at least 50% of the clustered proteomes to build sets of core proteins that include proteins from 95% of the clustered bacteria. These clusters typically capture >80% of proteins in the bacteria. Because these clusters have highly uniform length (the median cluster has >99% of its proteins at the mode length), short (<75% of mode length) or long (>133%) proteins are likely artifacts. Most “outlier” proteins are found in fewer than 10% of clusters, and “high-outlier” clusters are over-represented in a small fraction of proteomes, which often have poor proteome BUSCO fragment scores. Short-outlier proteins are artifacts; at least 80% of short-outlier genomes contain mode-length copies of the protein, which were missed because of frameshifts, termination codons, or initiation codon choice. MMseqs2 clustering with 50% participation provides robust sets of core bacterial proteins and can be used to identify lower-quality proteomes and proteins.