Quantitative and Computational Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
Nucleic Acids Res. 2018 Jul 2;46(W1):W215-W220. doi: 10.1093/nar/gky431.
The BaMM web server offers four tools: (i) de-novo discovery of enriched motifs in a set of nucleotide sequences, (ii) scanning a set of nucleotide sequences with motifs to find motif occurrences, (iii) searching with an input motif for similar motifs in our BaMM database with motifs for >1000 transcription factors, trained from the GTRD ChIP-seq database and (iv) browsing and keyword searching the motif database. In contrast to most other servers, we represent sequence motifs not by position weight matrices (PWMs) but by Bayesian Markov Models (BaMMs) of order 4, which we showed previously to perform substantially better in ROC analyses than PWMs or first order models. To address the inadequacy of P- and E-values as measures of motif quality, we introduce the AvRec score, the average recall over the TP-to-FP ratio between 1 and 100. The BaMM server is freely accessible without registration at https://bammmotif.mpibpc.mpg.de.
BaMM 网页服务器提供了四个工具：（i）在一组核苷酸序列中发现丰富基序的从头发现，（ii）用基序扫描一组核苷酸序列以查找基序出现，（iii）用输入基序在我们的 BaMM 数据库中搜索具有 >1000 个转录因子基序的相似基序，这些基序是从 GTRD ChIP-seq 数据库中训练得到的，（iv）浏览和关键字搜索基序数据库。与大多数其他服务器不同，我们不是通过位置权重矩阵（PWMs），而是通过阶数为 4 的贝叶斯马尔可夫模型（BaMMs）来表示序列基序，我们之前的研究表明，在 ROC 分析中，BaMMs 比 PWMs 或一阶模型表现要好得多。为了解决 P 值和 E 值作为基序质量度量的不足，我们引入了 AvRec 评分，即 1 到 100 之间的 TP 到 FP 比值的平均召回率。BaMM 服务器可在无需注册的情况下免费访问，网址为 https://bammmotif.mpibpc.mpg.de。
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