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

Anja Kiesel, Christian Roth, Wanwan Ge, Maximilian Wess, Markus Meier, Johannes Söding
2018 Nucleic Acids Research  
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  ...  ACKNOWLEDGEMENTS We thank our beta users for testing and feedback and Fëdor Kolpakov of BioUML (http://gtrd.biouml.org) for support with their GTRD database.  ... 
doi:10.1093/nar/gky431 pmid:29846656 pmcid:PMC6030882 fatcat:odz4yi2zbzghzcivzfm4oha62q

GTRD: a database on gene transcription regulation—2019 update

Ivan Yevshin, Ruslan Sharipov, Semyon Kolmykov, Yury Kondrakhin, Fedor Kolpakov
2018 Nucleic Acids Research  
for both human and mouse using position weight matrices from the HOCOMOCO database.  ...  Web interface to access GTRD was developed using the BioUML platform. It provides browsing and displaying information, advanced search possibilities and an integrated genome browser.  ...  ACKNOWLEDGEMENTS We would like to thank Dr Ivan Kulakovskiy and Dr Vsevolod Makeev for their collaboration between the HO-COMOCO and GTRD databases.  ... 
doi:10.1093/nar/gky1128 pmid:30445619 pmcid:PMC6323985 fatcat:has6jvpv2jcedk4kh637qnyf4y

Thermodynamic modeling reveals widespread multivalent binding by RNA-binding proteins [article]

Salma Sohrabi-Jahromi, Johannes Soeding
2021 bioRxiv   pre-print
However, current approaches to de-novo discovery of RNA binding motifs do not take multivalent binding into account.  ...  The BMF web server is accessible at https://bmf.soedinglab.org.  ...  Acknowledgements We thank Christian Roth for his help on AVXoptimization, web server implementation and for discussions on tool development and benchmark design.  ... 
doi:10.1101/2021.01.30.428941 fatcat:e5v4hlqdyfcb5g6z3vfhy5xpsq

Thermodynamic modeling reveals widespread multivalent binding by RNA-binding proteins

Salma Sohrabi-Jahromi, Johannes Söding
2021 Bioinformatics  
However, current approaches to de novo discovery of RNA binding motifs do not take multivalent binding into account.  ...  Our results demonstrate the importance of multivalent binding for RNA-binding proteins and highlight the value of bipartite motif models in representing the multivalency of protein-RNA interactions.  ...  Acknowledgements The authors thank Christian Roth for his help on AVX-optimization, web server implementation and for discussions on tool development and benchmark design.  ... 
doi:10.1093/bioinformatics/btab300 pmid:34252974 fatcat:5hh5pxdygrfnlgggpniumplide

Analysis of a Marseillevirus Transcriptome Reveals Temporal Gene Expression Profile and Host Transcriptional Shift

Rodrigo Araújo Lima Rodrigues, Amina Cherif Louazani, Agnello Picorelli, Graziele Pereira Oliveira, Francisco Pereira Lobo, Philippe Colson, Bernard La Scola, Jônatas Santos Abrahão
2020 Frontiers in Microbiology  
Eight million 75-bp-long nucleotide sequences were robustly mapped to all 457 genes initially predicted for Marseillevirus isolate T19, the prototype strain of the family, and we were able to assemble  ...  Cluster analysis indicated the existence of three main temporal categories of gene expression, early, intermediate and late, which were validated by quantitative reverse transcription polymerase chain  ...  De novo Motif Search and Statistical Analysis We used MEME (Motif Discovery Tool, version 5.0.4 (Bailey et al., 2009) for de novo motif prediction in the intergenic sequences of MRSV.  ... 
doi:10.3389/fmicb.2020.00651 pmid:32390970 pmcid:PMC7192143 fatcat:rh2dxxtymvf4xds73spj6byuxq