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Conservation of Protein Domains Over Different Proteins

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...

From DNA to Protein

From DNA to Protein

The flow of genetic information in cells from DNA to mRNA to protein is described by the central dogma, which states that genes specify the sequence of mRNAs, which in turn specify the sequence of amino acids making up all proteins. The decoding of one molecule to another is performed by specific proteins and RNAs. Because the information stored in DNA is so central to cellular function, it makes intuitive sense that the cell would make mRNA copies of this information for protein synthesis...

Conservation of Protein Domains

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Cis-regulatory Sequences

Cis-regulatory Sequences

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...

RNA Polymerase II Accessory Proteins

RNA Polymerase II Accessory Proteins

Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in...

DNA Replication

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DNA replication involves the separation of the two strands of the double helix, with each strand serving as a template from which the new complementary strand is copied. After replication, each double-stranded DNA includes one parental or “old” strand and one “new” strand. This is known as semiconservative replication. The resulting DNA molecules have the same sequence and are divided equally into the two daughter cells.
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Related Experiment Video

Updated: Feb 13, 2026

Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method

Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method

Published on: May 2, 2025

DNA Multiple Sequence Alignment Guided by Protein Domains: The MSA-PAD 2.0 Method.

Bachir Balech¹, Alfonso Monaco², Michele Perniola²

¹Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, CNR, Bari, Italy. balechbachir@gmail.com.

Methods in Molecular Biology (Clifton, N.J.)

|March 2, 2018

Summary

MSA-PAD 2.0 enhances DNA sequence alignment for metagenomics and phylogeny by using protein profiles. This upgraded framework offers faster, more robust alignments, including custom profiles, improving precision in sequence analysis.

Keywords:

Conserved protein domains Genomic rearrangement Multiple sequence alignment Phylogeny Sequence assignment

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Multiple sequence alignment (MSA) is crucial for DNA sequence analysis, including metagenomics and phylogeny.
Protein profile-guided alignments enhance precision and robustness in DNA multiple alignments.

Purpose of the Study:

To present the upgraded version of MSA-PAD (2.0), a DNA multiple sequence alignment framework.
To detail the framework's ability to align DNA sequences coding for protein domains using PFAM or custom annotations.
To introduce novel options for user-provided protein profiles to improve speed and flexibility.

Main Methods:

Utilizes two alignment strategies: "Gene" for coding domain order and "Genome" for genomic rearrangements.
Incorporates guidance from PFAM or user-defined protein domain annotations.
Allows alignment guided by user-provided protein profiles for custom analyses.

Main Results:

MSA-PAD 2.0 offers improved precision and robustness in DNA multiple sequence alignment.
The framework supports alignment of DNA sequences coding for single/multiple protein domains.
Novel options enable faster execution and integration of custom protein profiles.

Conclusions:

MSA-PAD 2.0 provides an enhanced, flexible, and efficient tool for DNA sequence alignment.
The framework's ability to use custom protein profiles expands its applicability in specialized research.
MSA-PAD 2.0 is freely available as a web application, facilitating its use in various DNA sequence analyses.