Motif Databasesdoi:10.1007/3-540-29623-9_7882A motif database contains representations of conserved sequences, for annotation of unknown sequences by comparison with individual, known sequences. Protein DatabasesSpringer Berlin Heidelberg
Firstly, we provide a comprehensive comparison of the coverage and quality of models available in different databases, showing that the public databases have comparable TFs coverage and better motif performance than commercial databases. Secondly, we compare different motif scanners showing that, ...
Motifer is a software tool able to find directly in nucleotide databases very distant homologues to an amino acid query sequence. It focuses searches on a specific amino acid pattern, scoring the matching and intervening residues as specified by the user. The program has been developed for search...
Comparsion of performance of motif databases should preferably be performed with the same motif scanning program, to separate the effect of the database from effects of different scanning programs. However, the two commercial motif databases: Transfac (Biobase) and MatBase (Genomatix); are each prov...
Optimally choosing pwm motif databases and sequence scanning approaches based on chip-seq data. BMC Bioinforma. 2015;16(1):1.Dabrowski,M., Dojer,N., Krystkowiak,I., Kaminska,B. and Wilczynski,B. (2015) Optimally choosing PWM motif databases and sequence scanning approaches based on ChIP-...
This overview describes PWMs and some of the most commonly used motif databases, as well as a few of their common applications.Gary DStormoCurrent protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]Stormo,G.D. (2015) DNA Motif Databases and Their Uses. In,...
structure analysis ‐ structural search in RNA motif databasesRmotifDB supporting searching for “nearest neighbors”of RNA structural motifs ‐ from its databasesearch engine based on blockmatchSummary This chapter contains sections titled: Introduction The Search Engine on RmotifDB The Search Engine ...
motifbreakR v2: expanded variant analysis including indels and integrated evidence from transcription factor binding databasesdoi:10.1093/bioadv/vbae162Coetzee, Simon GHazelett, Dennis JBioinformatics Advances
The main aim of this paper is to provide systematic compilation of a review on different approaches, databases and tools used in motif discovery.Tanmaya Kumar SahuCentre for Agricultural BioinformaticsA. R. RaoCentre for Agricultural BioinformaticsShuchi Vasisht...
Modified Prefix Span method for Motif Discovery in Sequence Databases. PRICAI, Springer-Verlag, 2417: 482-491.Kitakami, H., Kanbara, T., Mori, Y., Kuroki, S. and Ya- mazaki, Y., "Modified PrefixSpan Method for Motif Dis- covery in Sequence Databases," in Proc. of PRICAI2002, pp. ...