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The BaMM web server for de-novo motif discovery and regulatory sequence analysis
2018
Nucleic Acids Research
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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
2018
Nucleic Acids Research
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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]
2021
bioRxiv
pre-print
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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
2021
Bioinformatics
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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
2020
Frontiers in Microbiology
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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