(1) In this connection the question about the contribution of each word of length l (l-tuple) to the inhomogeneity of genetic text arises.
(2) A matching matrix species which k-tuples match each other.
(3) In our master-worker (MW) parallel implementation, a master process creates several worker processes, extracts a test sequence and multiple library sequences from a database and stores them in tuple space.
(4) An algorithm is described for generation of the long sequence written in a four letter alphabet from the constituent k-tuple words in the minimal number of separate, randomly defined fragments of the starting sequence.
(5) The present study proposes an algorithm that allows to overcome the computational difficulties occurring in the course of the method during reconstruction of the DNA sequence by its l-tuple composition.
(6) It is shown also that the biochemical problems connected with the loss of information about the l-tuple DNA composition during hybridization are not crucial and can be overcome by finding the maximal flow of minimal cost in the special graph.
(7) We then studied the distribution of oligonucleotides (or k-tuples) of each length in a subset of 129 complete mammalian genes spanning 0.607 Mb.
(8) It is shown that the efficiency of the statistical l-tuple filtration upon DNA database search is associated with a potential extension of the original four-letter alphabet and grows exponentially with increasing l. The formula that allows one to estimate the filtration parameters is presented.
(9) The concept of the algorithm enables operations with the k-tuple sets containing false positive and false negative k-tuples.
(10) In addition, one can match k-tuples or words instead of matching individual residues in order to speed the search.
(11) The frequency occurrences of K-tuple (overlapping sequences of defined length, K) were computed from the known human genome sequences.
(12) Parental bonding was assessed using the Parental Bonding Instrument [PBI; Parker, G. Tupling, H. & Brown, L.B.
(13) Each worker reads the test sequence and then repeatedly extracts library strings from tuple space, performs pairwise sequence comparison using a local comparison algorithm to generate a similarity score, and returns the similarity scores to tuple space.
(14) Average CLW distances for a variety of common word structures were more or less parallel to MDD distances for appropriately long t-tuples.
(15) relatively evenly distributed over a genome) versus non-stationary l-tuples has been introduced previously.
(16) Some of the rare 5-tuples identified by this strategy belonged to a portion of the nine base-pair binding site in promoters, which is also known as the octamer motif.
(17) Very few rare 5-tuples were identified; in addition, three oligonucleotides, reverse complements of rare 5-tuples, were found to have a frequency ranging between 0.582 and 0.671.
(18) We report that, through the use of alternative encodings of the DNA sequence in the complex plane, the number of FFTs performed can be traded off against (i) signal-to-noise ratio, and (ii) a certain degree of filtering for local similarity via k-tuple correlation.
(19) We defined as rare those 5-tuples having an observed frequency less than 50% of that expected by chance on the basis of base composition, and which had a reduction in frequency not attributable to CpG suppression or to coding constraints.
(20) Nucleotide or amino-acid sequences are interpreted as successions of words of length k (k-tuples) the frequencies of which are highly variable in different statistical populations of genes or proteins.