What is motif E value?
What is motif E value?
E-value: The E-value of the match of a sequence in a database to a group of motifs is defined as the expected number of sequences in a random database of the same size that would match the motifs as well as the sequence does and is equal to the combined p-value of the sequence times the number of sequences in the …
What is p-value in MEME?
The p-value tells you how well a particular site matches the PSSM found by MEME. The smaller the p-value, the more significant the match. The site p-value is described in the “Sites” sub-section of “Explanation of MEME Results” in the MEME output.
What is meme in bioinformatics?
MEME (Multiple EM for Motif Elicitation) is one of the most widely used tools for searching for novel ‘signals’ in sets of biological sequences. Applications include the discovery of new transcription factor binding sites and protein domains.
What is an enriched motif?
One current approach is to determine whether the regulatory sequences (e.g., promoters) of a set of genes have significantly higher than expected affinity for a regulatory protein or microRNA for which the DNA-binding motif is known. Such a motif is said to be “enriched” in the set of sequences.
What is Meme suite used for?
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.
What is a motif analysis?
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.
What is a motif in DNA?
Sequence motifs are short, recurring patterns in DNA that are presumed to have a biological function. Often they indicate sequence-specific binding sites for proteins such as nucleases and transcription factors (TF).
What does Fasta format look like?
What is FASTA format? A sequence in FASTA format begins with a single-line description, followed by lines of sequence data. The description line is distinguished from the sequence data by a greater-than (“>”) symbol in the first column. It is recommended that all lines of text be shorter than 80 characters in length.
How do you install meme suite?
Four steps are required to install the MEME Suite from a distribution tarball:
- Unzip and untar the distribution.
- Configure the installation using the command: configure.
- Build MEME Suite using the command: make.
- Test the MEME Suite build by using the command: make test .
- Install MEME Suite using the command: make install.
What is zinc finger motif?
A zinc finger is a small protein structural motif that is characterized by the coordination of one or more zinc ions (Zn2+) in order to stabilize the fold. It was originally coined to describe the finger-like appearance of a hypothesized structure from the African clawed frog (Xenopus laevis) transcription factor IIIA.
