Mining and gene ontology based annotation of SSR markers from expressed sequence tags of <i>Humulus lupulus</i>

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Title	Mining and gene ontology based annotation of SSR markers from expressed sequence tags of Humulus lupulus
Authors	Swati Singh^1,*, Ashutosh Mani¹, Anoop Chaturvedi²
Affiliation	¹Center of Bioinformatics,University of Allahabad,Allahabad, India-211002; ²Anoop Chaturvedi, Department of Statistics,University of Allahabad,Allahabad, India-211002.
Email	swatinatural@gmail.com; *Corresponding author
Article Type	Hypothesis
Date	Received January 12, 2012; Accepted January 17, 2012; Published February 03, 2012
Abstract	Humulus lupulus is commonly known as hops, a member of the family moraceae. Currently many projects are underway leading to the accumulation of voluminous genomic and expressed sequence tag sequences in public databases. The genetically characterized domains in these databases are limited due to non-availability of reliable molecular markers. The large data of EST sequences are available in hops. The simple sequence repeat markers extracted from EST data are used as molecular markers for genetic characterization, in the present study. 25,495 EST sequences were examined and assembled to get full-length sequences. Maximum frequency distribution was shown by mononucleotide SSR motifs i.e. 60.44% in contig and 62.16% in singleton where as minimum frequency are observed for hexanucleotide SSR in contig (0.09%) and pentanucleotide SSR in singletons (0.12%). Maximum trinucleotide motifs code for Glutamic acid (GAA) while AT/TA were the most frequent repeat of dinucleotide SSRs. Flanking primer pairs were designed in-silico for the SSR containing sequences. Functional categorization of SSRs containing sequences was done through gene ontology terms like biological process, cellular component and molecular function.
Keywords	Humulus lupulus, expressed sequence tag, molecular markers, simple sequence repeats.
Citation	Singh et al. Bioinformation 8(3): 114-122 (2012)
Edited by	P Kangueane
ISSN	0973-2063
Publisher	Biomedical Informatics
License	This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.