The comprehensive annotation of non-coding RNAs in newly sequenced genomes is still a largely unsolved problem because many functional RNAs exhibit not only poorly conserved sequences but also large variability in structure. In many cases, such as Y RNAs, vault RNAs, or telomerase RNAs, sequences differ by large insertions or deletions and have only a few small sequence patterns in common. Here...

Using a seed to rapidly “hit” possible homologies for further examination is a common practice to speed up homology search in molecular sequences. It has been shown that a collection of higher weight seeds have better sensitivity than a single lower weight seed at the same speed. However, huge memory requirements diminish the advantages of high weight seeds. This paper describes a twostage exte...

The protein sequence space is vast and diverse, spanning across different families. Biologically meaningful relationships exist between proteins at superfamily level. However, it is highly challenging to establish convincing relationships at the superfamily level by means of simple sequence searches. It is necessary to design a rigorous sequence search strategy to establish remote homology rela...

UNLABELLED New ideas, spaced seeds and gapped alignment before 6-frame translation are implemented for translated homology search in tPatternHunter. The new software compares favorably with tBLASTx. AVAILABILITY The software is free to academics at http://www.bioinformaticssolutions.com/downloads/ph-academic/ CONTACT [email protected].

Performing sequence homology searches against DNA or protein sequence databases is an essential bioinformatics task. Past research efforts have been primarily concerned with the development of sensitive and fast sequence homology search algorithms outside of the relational database management system (RDBMS). Oracle Data Mining (ODM) BLAST enables BLAST to be performed in a RDBMS. ODM BLAST reli...

During homologous recombination, RecA forms a helical filament on a single stranded (ss) DNA that searches for a homologous double stranded (ds) DNA and catalyzes the exchange of complementary base pairs to form a new heteroduplex. Using single molecule fluorescence imaging tools with high spatiotemporal resolution we characterized the encounter complex between the RecA filament and dsDNA. We p...

The theory of local homology modules was initiated by Matlis in 1974. It is a dual version of the theory of local cohomology modules. Mohammadi and Divaani-Aazar (2012) studied the connection between local homology and Gorenstein flat modules by using Gorenstein flat resolutions. In this paper, we introduce generalized local homology modules for complexes and we give several ways for computing ...

Genome annotation relies to a large extent on the recognition of homologs to already known genes. The starting point for such protocols is a collection of known sequences from one or more species, from which a model is constructed – either automatically or manually – that encodes the defining features of a single gene or a gene family. The quality of these models eventually determines the succe...

Conservation of microRNAs (miRNAs) among species suggests that they bear conserved biological functions. However, sequencing of new miRNAs has not always been accompanied by a search for orthologues in other species. I report herein the results of a systematic search for interspecies orthologues of miRNA precursors, leading to the identification of 35 human and 45 mouse new putative miRNA genes...

Escherichia coli RecA protein pairs homologous DNA molecules to form paranemic joints when there is an absence of a free end in the region of homologous contact. Paranemic joints are a key intermediate in homologous recombination and are important in understanding the mechanism for a search of homology. The efficiency of paranemic joint formation depended on the length of homology and the topol...