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Related Concept Videos

Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
Conservation of Protein Domains Over Different Proteins02:26

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 form...
Phylogenetic Trees03:21

Phylogenetic Trees

Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.The length of the branches can depict time or the relative amount of change among organisms. For instance, the branch length might indicate the number of amino acid changes in the sequence that underlies the...
Phylogenetic Trees03:21

Phylogenetic Trees

Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.The length of the branches can depict time or the relative amount of change among organisms. For instance, the branch length might indicate the number of amino acid changes in the sequence that underlies the...
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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.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
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Phylogeny

Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire...

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SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction.

Raffi Hagopian1, John R Davidson, Ruchira S Datta

  • 1Department of Bioengineering, University of California, Berkeley, CA 94720, USA.

Nucleic Acids Research
|May 1, 2010
PubMed
Summary

We developed SATCHMO-JS, a web server for simultaneous protein multiple sequence alignment (MSA) and phylogenetic tree construction. This tool significantly improves alignment accuracy compared to existing methods.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Accurate multiple sequence alignments (MSAs) and phylogenetic trees are crucial for understanding protein evolution.
  • Existing methods for simultaneous alignment and tree construction can be computationally intensive.

Purpose of the Study:

  • To introduce the SATCHMO-JS web server for efficient and accurate simultaneous estimation of MSAs and phylogenetic trees.
  • To improve upon the SATCHMO algorithm using a novel jump-start strategy.

Main Methods:

  • Developed the SATCHMO-JS web server, an extension of the SATCHMO algorithm.
  • Implemented a divide-and-conquer strategy to "jump-start" the alignment process.
  • Utilized hidden Markov models (HMMs) for HMM-HMM scoring and alignment.

Main Results:

  • SATCHMO-JS demonstrated statistically significant improvements in alignment accuracy.
  • Performance was evaluated against MUSCLE, MAFFT, ClustalW, and the original SATCHMO.
  • Benchmark dataset analysis showed superior accuracy of SATCHMO-JS.

Conclusions:

  • SATCHMO-JS offers a computationally efficient and more accurate approach for simultaneous MSA and phylogenetic tree inference.
  • The web server provides a valuable resource for the research community.
  • This method advances the field of phylogenetic analysis and protein sequence alignment.