MOTIVATION The increasing throughput of sequencing technologies offers new applications and challenges for computational biology. In many of those applications, sequencing errors need to be corrected. This is particularly important when sequencing reads from an unknown reference such as random DNA barcodes. In this case, error correction can be done by performing a pairwise comparison of all th...

We present a novel approach to comparing saccadic eye movement sequences based on the Needleman-Wunsch algorithm used in bioinformatics to compare DNA sequences. In the proposed method, the saccade sequence is spatially and temporally binned and then recoded to create a sequence of letters that retains fixation location, time, and order information. The comparison of two letter sequences is mad...

NEEDLEMAN, PHILIP, DELORES J. BLEHM, ANNE B. HARKEY, EUGENE M. JOHNSON. JR. AND STANLEY LANG : The metabolic pathway in the degradation of glyceryl trinitrate. J. Pharmacol. Exp. Ther. 179: 347-353, 1971. Glyceryl trinitrate (GTN) is degraded primarily in the liver by a partial denitration process catalyzed by organic nitrate reducta.se. The supporting evidence is as follows : 1) incubation of ...

Twenty-five years ago, in a commentary published in Pediatrics, Drs Needleman and Jackson1 asked whether we would still be treating lead poisoning in the 21st century. Unfortunately, despite considerable progress, our public health system is still failing to prevent children from being lead poisoned and the specter of lead poisoning continues to cast a shadow over the country: over 500 000 Amer...

Tryptophan-substitution mutagenesis was applied to the first and third transmembrane segments (S1 and S3) of a Shaker-type K(+) channel for the purpose of ascertaining whether these sequences are alpha-helical. Point mutants were examined for significant functional changes, indicated by the voltage-activation curves and gating kinetics. Helical periodicity of functional alteration was observed ...

One of the ubiquitous representation of long DNA sequence is dividing it into shorter k-mer components. Unfortunately, the straightforward vector encoding of k-mer as a one-hot vector is vulnerable to the curse of dimensionality. Worse yet, the distance between any pair of one-hot vectors is equidistant. This is particularly problematic when applying the latest machine learning algorithms to so...

In this article we propose a Fast Optimal Global Sequence Alignment Algorithm, FOGSAA, which aligns a pair of nucleotide/protein sequences faster than any optimal global alignment method including the widely used Needleman-Wunsch (NW) algorithm. FOGSAA is applicable for all types of sequences, with any scoring scheme, and with or without affine gap penalty. Compared to NW, FOGSAA achieves a tim...

The multilingual nature of the world makes translation a crucial requirement today. Parallel dictionaries constructed by humans are a widely-available resource, but they are limited and do not provide enough coverage for good quality translation purposes, due to out-of-vocabulary words and neologisms. This motivates the use of statistical translation systems, which are unfortunately dependent o...

In this paper, we implement Ant Colony Optimization (ACO) for sequence alignment. ACO is a meta-heuristic recently developed for nearest neighbor approximations in large, NP-hard search spaces. Here we use a genetic algorithm approach to evolve the best parameters for an ACO designed to align two sequences. We then used the best parameters found to interpolate approximate optimal parameters for...