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Phylogenetic Analysis of Blast Results

Brinkman, Fiona S Jorde, Lynn B. ; Dunn, Michael J. ; Subramaniam, Shankar ; Little, Peter F. R.

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, 2005, Vol.7, p.3093-3097

Chichester: John Wiley & Sons, Ltd

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  • Título:
    Phylogenetic Analysis of Blast Results
  • Autor: Brinkman, Fiona S
  • Jorde, Lynn B. ; Dunn, Michael J. ; Subramaniam, Shankar ; Little, Peter F. R.
  • Assuntos: Base sequence ; Comparative Analysis and Phylogeny ; Computational biology ; Evolution (Biology) ; Evolutionary genetics ; Genes ; Online databases ; Phylogeny ; Short Specialist Review
  • É parte de: Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, 2005, Vol.7, p.3093-3097
  • Descrição: BLAST (Basic Local Alignment Search Theorem) is one of the most elegant, and widely used bioinformatics analysis developed to date. Like many bioinformatic analyses, BLAST uses evolutionary theory as the basis for its assumptions. Therefore, an understanding of evolutionary theory is critical to the appropriate interpretation, and further analysis, of BLAST results. Viewing essentially one‐dimensional BLAST analysis from the perspective of a two‐dimensional phylogenetic analysis has a number of benefits including more accurate identification of the true “top hit”, delineation of gene families, identification of true homologs, and improved functional assignment of orthologs and paralogs. Performing such phylogenetic analyses has become easier, now that semiautomated methods have been developed that permit rough phylogenetic overviews of the data. However, it should be emphasized that phylogenetic analysis must often be customized for a given experiment or research question. Such issues are relevant not only to the further analysis of a BLAST output, but also to similar analyses of outputs from other widely used algorithms for rapid database search. Critical analysis of results is becoming increasingly important as sequence databases increase in both size and complexity – and as we begin to understand that even these large sequence databases are only scratching the surface of the true complexity and variety of sequences that exist in nature.
  • Editor: Chichester: John Wiley & Sons, Ltd
  • Idioma: Inglês
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  • Realização: ABCD-USP USP   Logos de Redes Sociais: Freepik

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