MOTIVATION Clustering methods including k-means, SOM, UPGMA, DAA, CLICK, GENECLUSTER, CAST, DHC, PMETIS and KMETIS have been widely used in biological studies for gene expression, protein localization, sequence recognition and more. All these clustering methods have some benefits and drawbacks. We propose a novel graph-based clustering software called COMUSA for combining the benefits of a coll...

Genetic variation and relationship among 28 mango germplasm were analyzed using Random Amplified Polymorphic DNA (RAPD). Out of 20 primers screened, four were selected, which gave 50 clear and bright fragments, out of which 48 fragments were considered polymorphic. The proportion of polymorphic loci and gene diversity values across all loci were 96% and 0.29, respectively. The UPGMA dendrogram ...

Identification and registration of new rice varieties are very important to be free from environmental effects and using molecular markers that are more reliable. The objectives of this study were, first, the identification and distinction of 40 rice varieties consisting of local varieties of Iran, improved varieties, and IRRI varieties using PIC, and discriminating power, second, cluster analy...

pathogenicity and genetic variability of 13 fusarium oxysporum isolates collected from sugar beet field of six provinces of iran during 1999- 2008 were evaluated. pathogenic variability of the isolates was determined using a root-dip assay in spore suspension in test tubes for four- week plants. the isolates were classified into strong and weak pathogenic groups. a total of 15 rapd primers were...

An alignment is an arrangement of two sequences which shows where the two sequences are similar, and where they differ. Here, in this paper, we report multiple alignments of few orthologous insulin sequences and construction of a python program based on average linkage clustering algorithm to generate clusters of significant similarities. Insulin sequences are extracted from uniprot knowledgeba...

Assessment of genetic diversity and population structure of germplasm collections plays a critical role in supporting conservation and crop genetic enhancement strategies. We used a cultivated lentil (Lens culinaris Medik.) collection consisting of 352 accessions originating from 54 diverse countries to estimate genetic diversity and genetic structure using 1194 polymorphic single nucleotide po...

An experiment was conducted to analyze the genetic diversity among 38 maize germplasm accessions of the maize germplasm bank of Department of Millets, TNAU, Coimbatore. Observations regarding 25 morphological traits were recorded and the data matrix was used for estimation of Euclidian distance by Un-weighted Paired Group Arithmetic Average (UPGMA) method. Clustering was done by Sequential Aggl...

Reconstruction of evolutionary relationships from noncontemporaneous molecular samples provides a new challenge for phylogenetic reconstruction methods. With recent biotechnological advances there has been an increase in molecular sequencing throughput, and the potential to obtain serial samples of sequences from populations, including rapidly evolving pathogens, is fast being realized. A new m...

We introduce a new technique to associate a spanning tree to the average linkage cluster analysis. We term this tree as the Average Linkage Minimum Spanning Tree. We also introduce a technique to associate a value of reliability to links of correlation based graphs by using bootstrap replicas of data. Both techniques are applied to the portfolio of the 300 most capitalized stocks traded at New ...

The genus Anthoxanthum s.l. (including Hierochloë) (Poaceae, Pooideae, Aveneae) comprises 35– 50 species and has a cosmopolitan distribution. Anthoxanthum alpinum was described as a diploid perennial that is distributed in northern Eurasia and in the high mountains of central and eastern Europe. Difficulties in finding reliable morphological differences between this taxon and the widespread tet...