Background: Micro RNAs (miRNAs) are a pivotal part of non-protein-coding endogenous small RNA molecules that regulate the genes involved in plant growth and development, and respond to biotic and abiotic environmental stresses posttranscriptionally.Objective: In the present study, we report the results of a systemic search for identifi cation of new miRNAs in B. rapa using homology-based ...

MOTIVATION Homology search methods are dominated by the central paradigm that sequence similarity is a proxy for common ancestry and, by extension, functional similarity. For determining sequence similarity in proteins, most widely used methods use models of sequence evolution and compare amino-acid strings in search for conserved linear stretches. Probabilistic models or sequence profiles capt...

The recombination protein RAD51 is a component of the meiotic recombination pathway and has been proposed to play a role in the homology search, a process by which homologous chromosomes find each other before they pair in the prophase of meiosis. To study the relationship between recombination and chromosome pairing, we examined the distribution of RAD51 foci on meiotic chromosomes in maize mu...

Daisychain is an interactive graph visualisation and search tool for custom-built gene homology databases. The main goal of to allow researchers working with specific genes identify homologs in other annotation releases. gene-centric representation includes local neighborhood distinguish orthologs paralogs by synteny. software supports genome sequences FASTA format GFF3 formatted files, the pro...

Dynamic Homology and Phylogenetic Systematics: A Unified Approach Using POY is a hybrid book: half algorithmic discussion and half reference manual for the cladogram search program POY. The first half of the book is dedicated to background and the algorithms that are used in POY. The second half details installation instructions for multiple platforms, suggested search techniques and over 250 c...

In this article, we show that magnitude homology and path are closely related, give some applications. We define differentials MH k ℓ ( G ) ⟶ − 1 $\operatorname{MH}^{\ell }_k(G) \longrightarrow \operatorname{MH}^{\ell -1}_{k-1}(G)$ between homologies of a digraph $G$ , which make them chain complexes. Then its $\mathcal {MH}^{\ell }_k(G)$ is non-trivial homotopy invariant in the context ‘homoto...

Non-coding RNAs (ncRNAs) are transcripts that do not code for proteins. Recent findings have shown that RNA-mediated regulatory mechanisms influence a substantial portion of typical microbial genomes. We present an efficient method for finding potential ncRNAs in bacteria by clustering genomic sequences based on homology inferred from both primary sequence and secondary structure. We evaluate o...

Since the discovery of the variety of functional roles performed by nonprotein-coding RNA (ncRNA), the search for homologous RNAs has been a problem of great interest in the field of bioinformatics. This thesis presents a new technique that uses an index-bases search tool to perform RNA homology search. A multiple sequence alignment of an RNA family is used to generate search patterns/descripto...