The BaMM web server for de-novo motif discovery and regulatory sequence analysis

Nucleic Acids Research
Anja KieselJohannes Söding

Abstract

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.

References

Feb 28, 2007·Genome Biology·Shobhit GuptaWilliam Stafford Noble
May 16, 2009·Science·Gwenael BadisMartha L Bulyk
May 22, 2009·Nucleic Acids Research·Timothy L BaileyWilliam S Noble
Oct 30, 2009·Nature·Remo RohsBarry Honig
May 11, 2011·Sub-cellular Biochemistry·Arttu Jolma, Jussi Taipale
Sep 20, 2012·Genome Research·Holger HartmannJohannes Söding
Feb 23, 2013·Journal of Bioinformatics and Computational Biology·Ivan KulakovskiyVsevolod Makeev
Sep 17, 2013·PLoS Computational Biology·Anthony Mathelier, Wyeth W Wasserman
Apr 24, 2015·Nucleic Acids Research·Alejandra Medina-RiveraJacques van Helden
Jun 12, 2016·Nucleic Acids Research·Matthias Siebert, Johannes Söding
Dec 8, 2016·Nucleic Acids Research·Ivan YevshinFedor Kolpakov
Feb 10, 2018·Cell·Samuel A LambertMatthew T Weirauch

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Citations

Nov 18, 2018·Nucleic Acids Research·Ivan YevshinFedor Kolpakov
May 12, 2020·Frontiers in Microbiology·Rodrigo Araújo Lima RodriguesJônatas Santos Abrahão
Jul 28, 2020·Nucleic Acids Research·Piroon JenjaroenpunIntawat Nookaew
Nov 9, 2019·Nucleic Acids Research·Oriol FornesAnthony Mathelier
Nov 25, 2020·Nucleic Acids Research·Semyon KolmykovFedor Kolpakov
Mar 12, 2021·Nucleic Acids Research·Grigorios Koulouras, Martin C Frith
May 1, 2021·NAR Genomics and Bioinformatics·Wanwan GeJohannes Söding
Aug 6, 2021·Briefings in Bioinformatics·Stefano CastellanaTommaso Mazza

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