VIRUS GENOME IMAGING VIA a2GRAMS: BUILDING A MATLAB TOOLBOX FOR PROKARYOTIC DNA ANALYSIS

C. Dantas Silva, E.A. Bouton, N.S. Santos-Magalhaes, H.M. de Oliveira

Resumo


Much of genomic signal analysis approaches  for feature extraction and functional cataloguing  have been focused on oligonucleotide  patterns in the  linear  primary  sequences of genomes.  New DNA-imaging tools  for genomic signal  processing  namely  codongrams  and  a2grams  had  recently  been  offered for extracting meaningful  genomic features  embedded  in DNA. A MatlabT M   toolbox  was implemented for allowing the image analysis of viruses and bacteriophages. Twenty different a2grams are defined for a genome, one for each amino acid (valgram  is an a2 gram for valine; alagram  is an a2 gram for alanine, etc.)  They  furnish information about  the distribution and occurrence  of the investigated amino acid. The codongram  describes the distribution of a specific codon through  the genome.  The a2gram  for a particular amino acid provides  information about the sections of the  DNA strand, which potentially leads to the synthesis  of such an amino acid.  DNA ×grams are among powerful visual tools for GSA like spectrograms,  which can  be applied  when searching  for particular nucleotide  patterns.   Among such  patterns, the  software  includes  built-in  options  the  following:  metgram  to  find out  potential start position of genes, Shine-Dalgarno sequence localizer (translation mRNA → protein), TATA  Box (replication DNA → mRNA), Enter  a sequence (DNA particular sequence finder).  A few genomes of viruses and  bacteriophage were made available  in the  DEMO  version:  Bacteriophage ΦX 174, phage MS2, Tomato Bushy  Stunt Virus  (TBSV),  Tobacco  Mosaic Virus  (TMV),  Phage  M13, and  Simian virus  SV40 (genome  lengths ranging  from 3,569 to  6,400 bp).   This  tool  is particularly helpful  for comparing  viruses, and it is also particularly valuable  for educational purposes.

Palavras-chave


GENOME IMAGING, Shine-Dalgarno sequence.

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DOI: https://doi.org/10.16923/reb.v3i1.181

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