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dc.contributor.authorMOKAYA, NYASIMI FESTUS
dc.date.accessioned2021-06-23T11:54:26Z
dc.date.available2021-06-23T11:54:26Z
dc.date.issued2020-09-23
dc.identifier.otherAN EXPANDED MOTIF ASSESSMENT AND RANKING SUITE FOR HUMAN AND INSECT RESEARCH
dc.identifier.otherNYASIMI FESTUS MOKAYA
dc.identifier.urihttp://elibrary.pu.ac.ke/handle/123456789/896
dc.descriptionMotif Assessment and Ranking Suite (MARS - http://bioinf.ict.ru.ac.za/) is a benchmark web server for MARSTools developed to evaluate, assess, rank and elucidate transcription factor (TF) binding motifs in Position Weight Matrix format. MARS evaluates TF motifs generated through motif discovery tools and selecting PWMs used in TF binding site (TFBS) prediction, thus solving the researcher’s motif finding and discovery problem. However, since its release in 2016, there has been a vast increase in ChIP-seq data and TF motifs, and the MARSTools dependencies extensively upgraded. Recently, there has been an increase in the relevance of insect research in different fields. This increase, coupled with the growing number of experimental data, motifs, and a curated genome, creates a need for a tool to assess the quality of models generated by different algorithms used to discover TFBS in insects. Raw ChIP-seq experiment data was obtained from Encyclopedia of DNA Elements (ENCODE), Gene Expression Omnibus Datasets and, Sequence Read Archives, and uniformly processed using the ENCODE ChIP-seq pipeline, which utilizes the SPP package and MACS2 peak callers. The motifs were then collated from various databases and converted to meme format using custom scripts. MARSTools was ported to Python3 and updated dependencies to the latest versions. Finally, the MySQL benchmark database and MARS web interface were updated to reflect the server's functionality and scope changes. The v2.0.0 release is a considerable expansion and update of the previous version. It now includes curated TFs, motifs and ChIP-seq data for Drosophila melanogaster - insect model organism. The updated MARS server will help users perform useful assessment and evaluation of motif models generated from different algorithms for both human and insect TFs.en_US
dc.description.abstractMotif Assessment and Ranking Suite (MARS - http://bioinf.ict.ru.ac.za/) is a benchmark web server for MARSTools developed to evaluate, assess, rank and elucidate transcription factor (TF) binding motifs in Position Weight Matrix format. MARS evaluates TF motifs generated through motif discovery tools and selecting PWMs used in TF binding site (TFBS) prediction, thus solving the researcher’s motif finding and discovery problem. However, since its release in 2016, there has been a vast increase in ChIP-seq data and TF motifs, and the MARSTools dependencies extensively upgraded. Recently, there has been an increase in the relevance of insect research in different fields. This increase, coupled with the growing number of experimental data, motifs, and a curated genome, creates a need for a tool to assess the quality of models generated by different algorithms used to discover TFBS in insects. Raw ChIP-seq experiment data was obtained from Encyclopedia of DNA Elements (ENCODE), Gene Expression Omnibus Datasets and, Sequence Read Archives, and uniformly processed using the ENCODE ChIP-seq pipeline, which utilizes the SPP package and MACS2 peak callers. The motifs were then collated from various databases and converted to meme format using custom scripts. MARSTools was ported to Python3 and updated dependencies to the latest versions. Finally, the MySQL benchmark database and MARS web interface were updated to reflect the server's functionality and scope changes. The v2.0.0 release is a considerable expansion and update of the previous version. It now includes curated TFs, motifs and ChIP-seq data for Drosophila melanogaster - insect model organism. The updated MARS server will help users perform useful assessment and evaluation of motif models generated from different algorithms for both human and insect TFs.en_US
dc.description.sponsorshipPwani Universityen_US
dc.language.isoenen_US
dc.publisherPwani Universityen_US
dc.subjectINSECT RESEARCHen_US
dc.subjectAN EXPANDED MOTIF ASSESSMENTen_US
dc.titleAN EXPANDED MOTIF ASSESSMENT AND RANKING SUITE FOR HUMAN AND INSECT RESEARCHen_US
dc.typeThesisen_US


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