biosequence analysis using profile hidden Markov models（使用隐马尔可夫模型分析序列）

最新推荐文章于 2023-08-27 02:48:58 发布

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最新推荐文章于 2023-08-27 02:48:58 发布

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分类专栏： bioinformatics

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HMMER是一个用于在序列数据库中搜索序列同源体和进行序列比对的工具，它利用profile隐藏马尔可夫模型（profile HMMs）方法。它可以与Pfam等数据库配合使用，也可直接处理查询序列，功能类似BLAST。HMMER设计用于尽可能敏感地检测远程同源体，并且现在的HMMER3版本速度接近BLAST。用户可以从European Bioinformatics Institute获取HMMER作为命令行工具或通过新搜索服务器使用。

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HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).

HMMER is often used together with a Pprofile database, such as Pfam or many of the databases that participate in Interpro. But HMMER can also work with query sequences, not just profiles, just like BLAST. For example, you can search a protein query sequence against a database with phmmer, or do an iterative search with jackhmmer.

HMMER is designed to detect remote homologs as sensitively as possible, relying on the strength of its underlying probability models. In the past, this strength came at significant computational expense, but as of the new HMMER3 project, HMMER is now essentially as fast as BLAST.

HMMER can be downloa