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Infect Genet Evol. 2014 Jan;21:287-94. doi: 10.1016/j.meegid.2013.11.018. Epub 2013 Nov 28.

Genome-wide scan for analysis of simple and imperfect microsatellites in diverse carlaviruses.

Author information

1
Department of Botany, Patna University, Bihar 800005, India.
2
Department of Biomedical Sciences, Shaheed Rajguru College of Applied Sciences for Women (SRCASW), University of Delhi, Vasundhara Enclave, New Delhi 110096, India.
3
Department of Biomedical Sciences, Shaheed Rajguru College of Applied Sciences for Women (SRCASW), University of Delhi, Vasundhara Enclave, New Delhi 110096, India. Electronic address: safdar_mgl@live.in.

Abstract

An exhaustive compilation and analysis of incidence, distribution and variation of simple sequence repeats (SSRs) in viruses are required to understand the evolution and functional aspects of repetitive sequences. Present study focuses on the analysis of SSRs in 32 species of carlaviruses. The full length genome sequences were assessed from NCBI (http://www.ncbi.nlm.nih.-gov/) and analyzed using IMEx software. Variance in incidence of SSRs was observed, independent of genome size. Though the conversion of SSRs to imperfect microsatellite or compound SSR is low; compound microsatellites constituted by variant motifs accounted for up to 12.5% of the SSRs. Mononucleotide A/T is most prevalent followed by dinucleotide GT/TG and trinucleotide AAG/GAA in these genomes. The SSR and cSSR are predominantly localized to the coding region RDRP (RNA dependent RNA polymerase) and ORF-6 (open reading frame). The relative frequency of different classes of simple and compound microsatellites has been highlighted in accordance with the biology of carlavirus. Characterization of such variations would be pivotal for deciphering the enigma of these widely used, but incompletely understood sequences.

KEYWORDS:

IMEx; Relative abundance; Relative density; cSSR%; dMAX

PMID:
24291012
DOI:
10.1016/j.meegid.2013.11.018
[Indexed for MEDLINE]
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