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MetaHMM: A webserver for identifying novel genes with specified functions in metagenomic samples

机译：Metahmm：用于鉴定具有特定功能的新型基因的网手器

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摘要

The fast and affordable sequencing of large clinical and environmental metagenomic datasets opens up new horizons in medical and biotechnological applications. It is believed that today we have described only about 1% of the microorganisms on the Earth, therefore, metagenomic analysis mostly deals with unknown species in the samples. Microbial communities in extreme environments may contain genes with high biotechnological potential, and clinical metagenomes, related to diseases, may uncover still unknown pathogens and pathological mechanisms in known diseases. While the species-level identification and description of the taxa in the samples do not seem to be possible today, we can search for novel genes with known functions in these samples, using numerous techniques, including artificial intelligence tools, like the hidden Markov models (HMMs). Here we describe a simple-to-use webserver, the MetaHMM, which is capable of homology-based automatic model-building for the genes to be searched for, and it also finds the closest matches in the metagenome. The webserver uses already highly successful building blocks: it performs multiple alignments by applying Clustal Omega, builds a hidden Markov model with HMMER components of hmmbuild and uses hmmsearch for finding similar sequences to the specified model in the metagenomes. The webserver is publicly available at https://metahmm.pitgroup.org.
机译：大型临床和环境偏心组织数据集的快速和实惠的测序在医疗和生物技术应用中开辟了新的视野。据信我们今天只描述了大约1％的微生物的地球，因此，偏见的分析主要涉及样品中未知的物种。极端环境中的微生物社区可能含有具有高生物技术潜力的基因，与疾病有关的临床偏见，可能揭示仍然未知的病原体和已知疾病的病理机制。虽然当今样品中的物种级别识别和分类群的描述似乎没有可能在这些样本中搜索具有已知功能的新基因，使用许多技术，包括人工智能工具，如隐藏的马尔可夫模型（ HMMS）。在这里，我们描述了一种易用的Web服务器，Metahmm，它能够用于搜索的基因的基于同源性的自动模型建设，并且还发现了MetageNome中最接近的比赛。 WebServer使用已经非常成功的构建块：它通过应用Clustal Omega执行多次对齐，构建具有HMMBuild的HMMER组件的隐马尔可夫模型，并使用HMMSearch在MetageNomes中的指定模型中查找类似的序列。 WebServer在HTTPS://metahmm.pitgroup.org上公开使用。

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