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MOFOID is a new server developed mainly for automated modeling of protein structures by their homology to the structures deposited in the PDB database. Selection of a template and calculation of the alignment is performed with the Smith-Waterman or Needleman-Wunsch algorithms implemented in the EMBOSS package. The final model is built and optimised with programs from the JACKAL package. The wid...

One of the basic tasks in bioinformatics is localizing a short subsequence S, read while sequencing, in a long reference sequence R, like the human geneome. A natural rapid approach would be finding a hash value for S and compare it with a prepared database of hash values for each of length |S| subsequences of R. The problem with such approach is that it would only spot a perfect match, while i...

Activity recognition in smart homes aims to infer the particular activities of the inhabitant, the aim being to monitor their activities and identify any abnormalities, especially for those living alone. In order for a smart home to support its inhabitant, the recognition system needs to learn from observations acquired through sensors. One question that often arises is which sensors are useful...

The classic algorithms of Needleman-Wunsch and Smith-Waterman find a maximum a posteriori probability alignment for a pair hidden Markov model (PHMM). To process large genomes that have undergone complex genome rearrangements, almost all existing whole genome alignment methods apply fast heuristics to divide genomes into small pieces that are suitable for Needleman-Wunsch alignment. In these al...

The identification of maximally homologous subsequences among sets of long sequences is an important problem in molecular sequence analysis. The problem is straightforward only if one restricts consideration to contiguous subsequences (segments) containing no internal deletions or insertions. The more general problem has its solution in an extension of sequence metrics (Sellers 1974; Waterman e...