meme motif discovery tool

Online Analysis Tools - Motifs

The "MEME output as HTML" file contains a detailed analysis of each of the motifs plus their Sequence Logos. At the top of the life is a buttom labelled "Search sequence databases for the best combined matches with these motifs using MAST." This will take you to theMAST (Motif Alignment and Search Tool) submission form.

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MEME Suite: tools for motif discovery and searching ...

May 20, 2009·The MEME Suite web server provides a unified portal for online discovery and analysis of sequence motifs representing features such as DNA binding sites and protein interaction domains. The popular MEME motif discovery algorithm is now complemented by the GLAM2 algorithm which allows discovery of motifs containing gaps. Three sequence scanning algorithms—MAST, FIMO and …

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Multiple EM for Motif Elicitation - Wikipedia

Multiple Expectation maximizations for Motif Elicitation (MEME) is a tool for discovering motifs in a group of related DNA or protein sequences. A motif is a sequence pattern that occurs repeatedly in a group of related protein or DNA sequences and is often associated with some biological function. MEME represents motifs as position-dependent letter-probability matrices which describe the ...

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MEME Suite: tools for motif discovery and searching

MEME Suite: tools for motif discovery and searching Timothy L. Bailey, Michael Boden, Fabian A. Buske, Martin Frith, Charles E. Grant, Luca Clementi, Jane Ren, Wilfred W. Li and William Stafford Noble. Nucleic Acids Research 37(Web server issue):W202-208, 2009.

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MEME Motif Formats - MEME Suite

The motif discovery tools in the MEME Suite output motifs in several more complex formats. All of these formats are also accepted by programs in the MEME Suite that take motifs as input. The HTML formats are designed for viewing by humans, whereas the text (.txt) and XML (.xml) formats are primarily designed to make it easier for third-party ...

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MEME SUITE: tools for motif discovery and searching ...

May 20, 2009·MEME and GLAM2 are tools for motif discovery, T omtom searches for similar motifs in databases of known motifs, FIMO, GLAM2SCAN and MAST search for occurrences of motifs in sequence databases, and GOMO provides associations between motifs and GO terms. The components of the MEME Suite are implemented in ANSI C as command line tools.

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Altmetric – MEME SUITE: tools for motif discovery and ...

The MEME Suite web server provides a unified portal for online discovery and analysis of sequence motifs representing features such as DNA binding sites and protein interaction domains. The popular MEME motif discovery algorithm is now complemented by the GLAM2 algorithm which allows discovery of motifs containing gaps.

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The MEME Suite: Motif-Based Sequence Analysis Tools ...

Initially described in 1994, MEME has been continually maintained and improved in the ensuing 16 years and is now probably the most widely used motif discovery tool, with a total of 1676 citations in Google Scholar and 800 users per month submitting over 200 queries per day to the MEME web service.

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MEME suite: Tools for motif discovery and searching

The MEME Suite web server provides a unified portal for online discovery and analysis of sequence motifs representing features such as DNA binding sites and protein interaction domains. The popular MEME motif discovery algorithm is now complemented by the GLAM2 algorithm which allows discovery of motifs containing gaps. Three sequence scanning algorithms-MAST, FIMO and …

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MEME -- Multiple EM for Motif Elicitation - Introduction

MEME -- Multiple EM for Motif Elicitation Motif discovery tool. motif distribution This is where you tell MEME how you believe occurrences of the motifs are distributed among the sequences. Selecting the correct type of distribution improves the sensitivity and quality of the motif search. ... The width of each motif that MEME reports will lie ...

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AMD, an Automated Motif Discovery Tool Using Stepwise ...

Numerous de novo motif discovery tools have been recently developed and quickly adapted by investigators in the community, including AlignACE [3], REDUCE [4], MEME [5], YMF [6],

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MEME Motif分析的并行运算 - 简书

Mar 02, 2021·并且很可能在之后anaconda里的meme更新后,再安装可能并没有我遇到的问题。 我当前需要使用的是meme 中的meme-chip 和 CentriMo两个功能。meme-chip封装了motif discovery和motif enrichment 两个功能。CentriMo 单用于motif enrichment. 但是当前conda 安装的meme,没法使用meme-chip和CentriMo 。

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MEME Motif分析的并行运算 - 简书

Mar 02, 2021·并且很可能在之后anaconda里的meme更新后,再安装可能并没有我遇到的问题。 我当前需要使用的是meme 中的meme-chip 和 CentriMo两个功能。meme-chip封装了motif discovery和motif enrichment 两个功能。CentriMo 单用于motif enrichment. 但是当前conda 安装的meme,没法使用meme-chip和CentriMo 。

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mCUDA-MEME - Yongchao Liu Personal

mCUDA-MEME is an ultrafast scalable motif discovery algorithm based on MEME (version 4.4.0) algorithm for multiple GPUs using a hybrid combination of CUDA, MPI and OpenMP parallel programming models.This algorithm is a further extension of CUDA-MEME with respect to accuracy and speed and has been tested on a GPU cluster with eight compute nodes and two Fermi-based Tesla …

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AMD, an Automated Motif Discovery Tool Using Stepwise ...

Numerous de novo motif discovery tools have been recently developed and quickly adapted by investigators in the community, including AlignACE [3], REDUCE [4], MEME [5], YMF [6],

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MEME Motif分析的并行运算 - 简书

Mar 02, 2021·并且很可能在之后anaconda里的meme更新后,再安装可能并没有我遇到的问题。 我当前需要使用的是meme 中的meme-chip 和 CentriMo两个功能。meme-chip封装了motif discovery和motif enrichment 两个功能。CentriMo 单用于motif enrichment. 但是当前conda 安装的meme,没法使用meme-chip和CentriMo 。

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Multiple EM for Motif Elicitation - Wikipedia

Multiple Expectation maximizations for Motif Elicitation (MEME) is a tool for discovering motifs in a group of related DNA or protein sequences. A motif is a sequence pattern that occurs repeatedly in a group of related protein or DNA sequences and is often associated with some biological function. MEME represents motifs as position-dependent letter-probability matrices which describe the ...

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ROSALIND | New Motif Discovery

Jun 19, 2013·Each motif in MEME is assigned an expected value (E), which is the likelihood of it occurring by chance. This denotes the statistical significance of the motif. GLAM2 assigns scores instead of e-values: the score favours alignment of similar residues, and disfavours insertions and deletions. Problem. The novel-motif finding tool MEME can be ...

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MODSIDE: a motif discovery pipeline and similarity ...

Oct 19, 2018·Motif discovery MEME. MEME (Multiple Expectation Maximization for Motif Elicitation) is a well-known motif discovery tool developed for targeting un-gapped motifs in unaligned DNA or protein sequences . MEME algorithm is based on a profile-based method that implemented the expectation maximization (EM) .

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MEME Suite: tools for motif discovery and searching ...

May 20, 2009·The MEME Suite web server provides a unified portal for online discovery and analysis of sequence motifs representing features such as DNA binding sites and protein interaction domains. The popular MEME motif discovery algorithm is now complemented by the GLAM2 algorithm which allows discovery of motifs containing gaps. Three sequence scanning algorithms—MAST, FIMO and …

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Meme Discovering And Analyzing Dna And Protein Sequence ...

Meme Chip Motif Discovery Based On The Underlying Sequences Figure 1 From Meme Chip Motif Analysis Of Large Dna ... Table 3 From Motifsim A Web Tool For Detecting Similarity Sequence Motifs Identified In Srnas By Meme Overrepresented Related : Meme Discovering And Analyzing Dna And Protein Sequence Motifs. Tags: ...

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(PDF) MEME SUITE: tools for motif discovery and searching ...

MEME (2) and GLAM2 (3) are tools for motif MEME motif discovery algorithm is now com- discovery, TOMTOM (4) searches for similar motifs in data- plemented by the GLAM2 algorithm which allows bases of known motifs, FIMO, GLAM2SCAN (3) and discovery of motifs containing gaps.

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Chapter 2: Sequence Motifs – Applied Bioinformatics

2.6.2 MEME and the EM Algorithm. One of the most widely used software tools for motif discovery is MEME: Multiple EM for Motif Elicitation. MEME uses Expectation Maximization to find the best binding sites . The algorithm computes the parameters that maximize the expected value of …

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MEME - Motif discovery tool

Apr 02, 2002·MEME - Motif discovery tool. MEME version 3.0 (Release date: 2002/04/02 00:11:59) ... For use with BLOCKS tools, MEME prints the occurrences of the motif in BLOCKS format. You can convert these blocks to PSSMs (position-specific scoring …

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bio.tools · bio.tools

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