We survey recent work in the seeding of alignments, particularly the follow-ups from the 2002 work of Ma, Tromp and Li that brought the concept of spaced seeds into the bioinformatics literature [25]. Our focus is on the extensions of this work to increasingly complicated models of alignments, coming up to the most recent efforts in this area.

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].

Multiple sequence alignment is a classical and challenging task for biological sequence analysis. The problem is NP-hard. The full dynamic programming takes too much time. The progressive alignment heuristics adopted by most state of the art multiple sequence alignment programs suffer from the 'once a gap, always a gap' phenomenon. Is there a radically new way to do multiple sequence alignment?...

MOTIVATION Standard search techniques for DNA repeats start by identifying small matching words, or seeds, that may inhabit larger repeats. Recent innovations in seed structure include spaced seeds and indel seeds which are more sensitive than contiguous seeds. Evaluating seed sensitivity requires (i) specifying a homology model for alignments and (ii) assigning probabilities to those alignment...

The paper aims at the investigation of free word order. It concentrates on the relationship between (formal) dependencies and word order. The investigation is performed by means of a semi-automatic application of a method of analysis by reduction to Czech syntactically annotated data. The paper also presents the analysis of introspectively created Czech sentences demonstrating complex phenomena...

With a sharp increase of available DNA and protein sequence data, new precise and fast similarity search methods are needed for largescale genome and proteome comparisons. Modern seed-based techniques of similarity search (spaced seeds, multiple seeds, subset seeds) provide a better sensitivity/specificity ratio. We present an implementation of such a seed-based technique on a parallel speciali...

Rambutan tree (Nepheliumlappaceum L.) is an important but a lesser known fruit tree in Ghana and has several nutritional and medicinal uses. Efforts to establish plantation of Rambutan in Ghana to ensure its sustainable use is challenged with unavailable planting materials because the seeds are recalcitrant in nature, loses viability easily when exposed to dryness. Seeds are therefore sown dire...