Nucleic acids and nucleotides relationship memes

Nucleotides and Nucleic Acids

nucleic acids and nucleotides relationship memes

Nucleic Acids (RNA and DNA) are made up of a series of nucleotides. The center of an amino acid is the carbon bonded to four different groups. The fourth. The MEME Suite is a powerful, integrated set of web-based tools for studying Nucleic Acids Research, Volume 43, Issue W1, 1 July , Pages W39–W49, .. and maximum motif widths to 10 and 25 amino acids, respectively. .. [ Relationship between sonographic markers and fetal chromosome. DNA itself is a nucleic acid, that's why it's called Deoxyribonucleic Acid. Nucleotides are a part of DNA.

The meme web server came online in and is now widely used, with almost 20 unique users in alone.

MAVL and StickWRLD: visually exploring relationships in nucleic acid sequence alignments

Using the MEME Suite The web-based version of the MEME Suite includes 13 tools 12345678910111213 for performing motif discovery, motif enrichment analysis, motif scanning and motif—motif comparisons Figure 1. For motif discovery and motif enrichment analyses, the user provides a set of unaligned DNA, RNA or protein sequences Figure 1upper left.

Typically, these sequences might be ChIP-seq peak regions, cross-linking sites from a CLIP-seq experiment, promoters of co-expressed genes or proteins sharing a common function such as being modified by the same kinase. Motif discovery finds de novo motifs in the user-provided sequences Figure 1upper middle. These motifs can then be input directly to the motif scanning and motif comparison tools of the MEME Suite Figure 1right to identify other proteins or genomic sequences that may contain the discovered motifs, or to determine if the motifs are similar to previously studied motifs.

Nucleosides and Nucleotides

The MEME Suite provides a large number of proteomic and genomic sequence databases Figure 1top right for motif scanning and many motif databases for motif comparison Figure 1bottom right. The four different motif discovery algorithms suit different purposes.

nucleic acids and nucleotides relationship memes

Finally, meme-chip is adapted to very large datasets that cannot be handled by meme, and it actually performs motif discovery, motif enrichment and motif comparison on its input sequences, producing a fully integrated report. A comprehensive protocol for using meme-chip has recently been published Motif enrichment analysis tests known motifs for enrichment in a set of user-provided sequences. Sensitivity is highest with CentriMo, which leverages the extra information sometimes contained in the position of the motif within each of the input sequences.

The sequences input to CentriMo must all have the same length, which is not the case with the less sensitive motif enrichment algorithm AME.

The SpaMo algorithm looks for preferred spacings in the input sequences between two motifs, rather than enrichment of a single motif. Finally, the gomo algorithm performs motif scanning of promoter sequences followed by a Gene Ontology enrichment analysis, so it is often applied to de novo discovered motifs to identify their possible biological functions.

Motif scanning involves identifying locations of occurrences of a given set of motifs within a given set of sequences. As with motif discovery, the four motif scanning tools suit distinct purposes Figure 1middle right. The fimo algorithm identifies all individual motif occurrences and is the method of choice for scanning genomes.

Its output can be uploaded to the UCSC genome browser for viewing. In contrast, the mast algorithm is sequence oriented and assigns each sequence in the selected database a score based on how well it matches all of the motifs input by the user. Thus, mast is most suited to scanning short sequences such as proteins or promoters.

MAVL and StickWRLD: visually exploring relationships in nucleic acid sequence alignments

The mcast algorithm scans genomes for clusters containing multiple matches to any or all of the motifs in its input. It was designed for detecting cis-regulatory modules CRMs bound by a known set of transcription factors. Finally, the glam2scan algorithm is similar to fimo but is designed to accept glam2 motifs; hence, the resulting motif matches may contain insertions and deletions.

The MEME Suite's motif comparison tool, Tomtom, allows the user to compare motifs discovered by the suite, by other tools, or taken from the literature to all of the motifs in a selected database of motifs Figure 1bottom right.

For example, Tomtom can be used to determine if a reported consensus sequence for a transcription factor motif matches any known motifs in databases of motifs produced using SELEX or protein-binding microarrays. Tomtom aligns each input motif with each motif in the selected database and reports the most similar pairs, along with estimates of the statistical significance of each match. Users can also use the MEME Suite with motifs generated by other motif analysis tools or taken directly from the literature Figure 1bottom left.

As described in the next section, the web server allows user-specified motifs to be input in many convenient formats.

Although omitted from Figure 1 for clarity, the motif scanning tools also allow for user-provided sequences, and the motif comparison tool allows for uploading user-provided motif databases.

Within each of the groupings of MEME Suite motif analysis tools discovery, enrichment, scanning, comparisonthe user interfaces are consistent and flexible.

For example, you can input sequences required by the first three groupings either by selecting a file for upload or by typing or cut-and-paste.

nucleic acids and nucleotides relationship memes

Base-pairing holds the double-stranded DNA molecule together. All RNA is single-stranded a single long chain of nucleotides.

What is the relationship between the nucleotides, nucleic acids, and DNA?

However, one section of the RNA molecule can base-pair with another section. This molecule, called tRNA base-pairs with itself to form a cloveleaf structure. Each circle represents a single nucleotide A, U, c, or G.

nucleic acids and nucleotides relationship memes

Lines that connect different nucleotides represent the hydrogen bonds of base-pairing. In nature, the cloverleaf folds up into a "L" shape. This is the same molecule represented in the figure at left.

nucleic acids and nucleotides relationship memes

The inset is another kind of depiction of the structure of tRNA, called a space-filling model. There are three kinds of RNA; the main purpose of all of these is protein synthesis. Ribosomes are large complexes consisting of multiple different RNA molecules and many different protein molecules.

To learn more about this process, read about protein synthesis. All DNA is double-stranded.

nucleic acids and nucleotides relationship memes

The two strands are antiparallel pointing in opposite directions. The backbone of each strand is the chain of sugars and phosphates.

What is the relationship between the nucleotides, nucleic acids, and DNA? | Socratic

The nitrogenous bases of each strand are in the center, pointing toward the other strand. Each nitrogenous base forms hydrogen bonds with the complementary base pair on the opposite strand.

Because the double-stranded DNA molecule twists around, it actually looks more like a spiral staircase than like a ladder. DNA is referred to as the "double-helix" because of this twist. Click Here for an enlarged DNA structure image. DNA is the genetic material in cells - the essential part of the chromosomes.

  • INTRODUCTION

Chromosomes are very long double-helixes of DNA - a long pair of chains of nucleotides. Chromosomes in eukaryotic cells are linear - they have two ends. Chromosomes in bacteria are circular - the two ends are attached.