Work in motif in raw

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Aug 6th, 2022
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How to work in motif in raw

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NARRATOR: The following content is provided under a Creative Commons license. Your support will help MIT OpenCourseWare continue to offer high-quality educational resources for free. To make a donation, or view additional materials from hundreds of MIT courses, visit MIT OpenCourseWare at ocw.mit.edu. PROFESSOR: All right, we should get started. So itamp;#39;s good to be back. Weamp;#39;ll be discussing DNA sequence motifs. Oh yeah, we were, if youamp;#39;re wondering, yes, the instructors were at the awards on Sunday. It was great. The pizza was delicious. So today, weamp;#39;re going to be talking about DNA and protein sequence motifs, which are essentially the building blocks of regulatory information, in a sense. Before we get started, I wanted to just see if there are any questions about material that Professor Gifford covered from the past couple days? No guarantees Iamp;#39;ll be able to answer them, but just general things related to transcriptome analysis, or PCA? Anythin

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FIMO outputs a GFF3 file (fimo. gff) that contains one line for each docHub match to a motif. FIMO Output Formats - MEME Suite MEME Suite meme doc fimo-output-format MEME Suite meme doc fimo-output-format
What is a Q-Value? A p-value is an area in the tail of a distribution that tells you the odds of a result happening by chance. A Q-value is a p-value that has been adjusted for the False Discovery Rate(FDR). The False Discovery Rate is the proportion of false positives you can expect to get from a test. Q-Value: Definition and Examples - Statistics How To Statistics How To q-value Statistics How To q-value
Motif Enrichment Analysis (MEA) seeks to determine which DNA-binding transcription factors control the transcription of a set of genes by detecting enrichment of known binding motifs in the genes regulatory regions. Motif Enrichment Analysis: a unified framework and an evaluation on BMC Bioinformatics - BioMed Central articles BMC Bioinformatics - BioMed Central articles
The parameter --max-stored-scores sets the maximum number of motif occurrences that will be retained in memory. It defaults to 100,000. FIMO - MEME Suite mit.edu memev4.11.4 share doc fimo mit.edu memev4.11.4 share doc fimo
The q-value is similar to a p-value but corrected for multiple testing. Like a p-value, a q-value of 0.01 or less is a reasonable threshold for significance. However, to compute q-values, FIMO has to hold all the matches in memory. When scanning a full genome this can easily require tens of GB of memory. FIMO Tutorial - MEME Suite MEME Suite meme doc fimo-tutorial MEME Suite meme doc fimo-tutorial
The Q-value in an undisturbed rock mass may be different. The Q-system is a classification system for rock masses with respect to stability of underground openings. Based on estimation of six rock mass parameters, a Q-value for a rock mass can be calculated. This value gives a description of the rock mass quality. Using the Q-system - NGI NGI bilder bygg-og-anlegg handbo NGI bilder bygg-og-anlegg handbo
The MEME Suite allows you to discover novel motifs in collections of unaligned nucleotide or protein sequences, and to perform a wide variety of other motif-based analyses. It provides motif discovery algorithms using both probabilistic (MEME) and discrete models (STREME), which have complementary strengths. MEME Suite: Introduction meme-suite.org meme-suite.org

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