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Protein Families02:47

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Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key...
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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.
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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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An Integrated Approach for Microprotein Identification and Sequence Analysis
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MSA-PAD: DNA multiple sequence alignment framework based on PFAM accessed domain information.

Bachir Balech1, Saverio Vicario2, Giacinto Donvito3

  • 1Istituto di Biomembrane e Bioenergetica and.

Bioinformatics (Oxford, England)
|March 31, 2015
PubMed
Summary
This summary is machine-generated.

We introduce MSA-PAD, a novel DNA multiple sequence alignment tool. It leverages protein domain information for accurate DNA sequence alignment in gene or genome modes.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Multiple sequence alignment (MSA) is fundamental for understanding DNA and protein sequence evolution.
  • Accurate alignment of DNA sequences, especially those encoding protein domains, remains a challenge.
  • Existing tools may not fully leverage protein domain information for DNA sequence alignment.

Purpose of the Study:

  • To present the MSA-PAD application, a new framework for DNA multiple sequence alignment.
  • To enable alignment of DNA sequences based on conserved protein domain information.
  • To provide flexible alignment options for both single and multiple protein domains within DNA sequences.

Main Methods:

  • Development of the MSA-PAD application.
  • Integration of PFAM protein domain information into the alignment process.
  • Implementation of two distinct alignment modes: gene mode and genome mode.

Main Results:

  • MSA-PAD successfully aligns DNA sequences by utilizing PFAM protein domain data.
  • The application supports the alignment of DNA sequences encoding single or multiple protein domains.
  • Two operational modes (gene and genome) offer versatility for different research needs.

Conclusions:

  • MSA-PAD offers an effective solution for DNA multiple sequence alignment using protein domain information.
  • The tool enhances the accuracy and utility of DNA sequence alignments in genomic research.
  • MSA-PAD provides a valuable resource for researchers studying gene and genome evolution.