63. Virus Genome Imaging via a2grams


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 Matlab 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 a2gram for valine; alagram is an a2gram 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 to protein), TATA Box (replication DNA to mRNA), Enter a sequence (DNA particular sequence finder).
A few genomes of viruses and bacteriophage were made available in the DEMO version:
Bacteriophage phiX174, 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.