Correct motif in 602

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How to Correct motif in 602

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okay so um as i talk about um in part one were like doing the alignment and quality control of our ar chipset data and then in part two its more like looking over public available ar data set to get a feeling of some quality control but as we mentioned for chipseek we still want some downstream analysis followed by our part one and in lecture you talked we talked about motive finding and so so this picture is copied from shirley slide um so you can imagine tf2 as our ar transcriptional factor and when we put on ar if if there are some other transcriptional factors that are binding with it or like co-interacting with it binding to the same dna region then since theyre so close even though our antibody only binds to tf2 tf1 and its dna will be put down as well so thats how we define co-interacting tfs and then by because if you take a look at our output bat file from part one its essentially just some chromosome start restart of a peak region and end off a peak region and then we al

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What is motif Discovery?

Motif discovery (or motif finding) in biological sequences can be defined as the problem of finding short similar sequence elements (building the motif) shared by a set of nucleotide or protein sequences with a common biological function.

How do you find the motif of a DNA?

While one can use established lists of motifs to search ones DNA sequence one can also discover them directly. In order to do this one has to derive a consensus sequence or probability matrix. In the case of bacterial proteins for which the binding sites have been determined good places to start are the E.

What is a motif in sequence alignment?

Introduction. Sequence motifs are commonly described as relatively short conserved regions within a protein or DNA sequence [1]. These regions are of functional importance: they serve as binding sites for ligands or transcription factors, and as catalytic sites or structural elements.

What is motif in a sequence?

A DNA sequence motif is a subsequence of DNA sequence that is a short similar recurring pattern of nucleotides, and it has many biological functions 1. A DNA motif refers to a short similar repeated pattern of nucleotides that has biological meaning.

What is a protein motif example?

A motif is a short conserved sequence pattern associated with distinct functions of a protein or DNA. It is often associated with a distinct structural site performing a particular function. A typical motif, such as a Zn-finger motif, is ten to twenty amino acids long.

What is the structure of motif?

What is a structure motif? Structure motifs are the spatial or 3D arrangement of a small number of amino acids (at least 2) that have significance - e.g., form a catalytic or binding site.

What is the purpose of motif finding?

Motif discovery plays a vital role in identification of Transcription Factor Binding Sites (TFBSs) that help in learning the mechanisms for regulation of gene expression. Over the past decades, different algorithms were used to design fast and accurate motif discovery tools.

How do you find motifs?

If there was an object or idea that kept popping up in the text, thats your motif. The second way is to work forward. You first look for the objects or ideas that appear over and over again. Then you link them to a theme.

What are the different methods of motif finding?

Different approaches of finding motifs in DNA sequences have been introduced in literature. They can be classified into three section with respect to the type of each search technique - Enumerative Search, Deterministic Search and Stochastic Search. Enumerative search is usually used for consensus representations.

What is a motif in protein sequence?

A protein sequence motif, or pattern, can be broadly defined as a set of conserved amino acid residues that are important for protein function and are located within a certain distance from each other. These motifs often can provide some clues to the functions of otherwise uncharacterised proteins.

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