In silico comparison of simple sequence repeats in high nucleotides-rich genomes of microorganism.
This study determined the distribution of a specific group of Simple Sequence Repeats (SSRs), in genome sequences of 7 chromosomes (Shigella flexneri 2a str 301 and 2457 T, Shigella sonnei, E. coli K12, M. tuberculosis, M. leprae and S. saprophytycus) have downloaded from the GenBank database for identifying abundance, distribution and composition of SSRs. The data obtained in the present study show that: (i) Tandem repeats are widely distributed throughout the genomes. (ii) SSRs are differentially distributed among coding and non-coding regions in investigated Shigella genomes. (iii) Total frequency of SSRs in non-coding regions is higher than coding regions. (iv) In all investigated chromosomes ratio of Tri-nucleotide SSRs are much higher than randomized genomes and Di nucleotide SSRs are lower. (v) Ratio of total and mono-nucleotide SSRs in real genome is higher than randomized genomes in E. coli K12, Sh. flexneri str 301 and S. saprophyticus, while it is lower in Sh. flexneri str 2457T, Sh. sonnei and M. tuberculosis and it is approximately same in M. leprae. (vi) Frequency of codon repetitions are vary considerably depending on the type of encoded amino acid.
Rahim
Fakher
F
Physiology Research Center, Ahwaz Jondishpour University of Medical Sciences, Ahwaz, Iran.
D001419:Bacteria / Q000235:genetics*; D002876:Chromosomes, Bacterial / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D048168:Escherichia coli K12 / Q000235:genetics; D016680:Genome, Bacterial; D018598:Minisatellite Repeats; D009166:Mycobacterium leprae / Q000235:genetics; D009169:Mycobacterium tuberculosis / Q000235:genetics; D012763:Shigella flexneri / Q000235:genetics; D012764:Shigella sonnei / Q000235:genetics; D013210:Staphylococcus / Q000235:genetics
D004269:DNA, Bacterial