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Related Concept Videos

RNA Splicing01:32

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Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
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Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
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When protons A and X are coupled, their nuclear spin energy levels are slightly modified. This is because the energy required to excite proton A to a spin state parallel to proton X is slightly different from the energy required for it to become anti-parallel to spin X. Consequently, there are two possible excitation frequencies for A (A1 and A2), depending on the spin state of X, and vice versa. The mutual nature of coupling implies that the difference between frequencies A1 and A2, indicated...
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Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation
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SpliVert: A Protein Multiple Sequence Alignment Refinement Method Based on Splitting-Splicing Vertically.

Qing Zhan1, Yilei Fu1, Qinghua Jiang2

  • 1School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China.

Protein and Peptide Letters
|August 7, 2019
PubMed
Summary
This summary is machine-generated.

A new method called SpliVert refines protein multiple sequence alignments (MSA) by splitting them vertically. This approach improves alignment accuracy by focusing on specific regions, outperforming traditional horizontal splitting methods.

Keywords:
Proteinmultiple sequence alignmentprogressive alignmentrealignrefinementsplitting-splicing vertically.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Multiple Sequence Alignment (MSA) is crucial for biological analyses, with accuracy directly impacting downstream results.
  • Existing protein MSA refinement methods often use horizontal splitting, which can fail to account for regional sequence conservation variations.
  • This limitation can lead to uncorrectable errors in residue-residue or residue-gap pairings.

Purpose of the Study:

  • To introduce a novel vertical splitting-splicing strategy for refining protein multiple sequence alignments.
  • To address the limitations of conventional horizontal splitting methods in MSA refinement.
  • To enhance the accuracy and reliability of biological sequence alignments.

Main Methods:

  • A new method, SpliVert, is proposed for MSA refinement using a vertical splitting-splicing approach.
  • The alignment is vertically divided into three segments.
  • The middle segment is realigned independently after gap removal, then spliced back with the original outer segments.

Main Results:

  • SpliVert was tested on leading MSA tools using standard benchmarks, showing comparable or improved average scores (SP and TC).
  • The refinement strategy demonstrated effectiveness when appropriate splitting proportions were used.
  • SpliVert-refined alignments outperformed alignments directly produced by original MSA tools.

Conclusions:

  • Vertical splitting and partial realignment is an effective strategy for refining protein multiple sequence alignments.
  • The SpliVert method offers a promising advancement in improving MSA accuracy.
  • This technique enhances the credibility of subsequent bioinformatics analyses reliant on accurate alignments.