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Alignathon: A competitive assessment of whole genome alignment methods

Multiple sequence alignments (MSAs) are a prerequisite for a wide variety of evolutionary analyses. Published assessments and benchmark datasets for protein and, to a lesser extent, global nucleotide MSAs are available, but less effort has been made to establish benchmarks in the more general problem …

Two horizontally stacked fuzzy double helixs

Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment

Motivation: Multiple sequence alignment is a cornerstone of comparative genomics. Much work has been done to improve methods for this task, particularly for the alignment of small sequences, and especially for amino acid sequences. However, less work has been done in making promising methods that …

Medaka fish

The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates

We have developed several new methods to investigate transcriptional motifs in vertebrates. We developed a specific alignment tool appropriate for regions involved in transcription control, and exhaustively enumerated all possible 12-mers for involvement in transcription by virtue of their mammalian conservation. We then used deeper …