To overcome the time consumption of Smith Waterman algorithm, Lipman and Pearson proposed FASTA tool in 1985, which takes a given nucleotide or amino acid sequence and searches a corresponding sequence database by using local sequence alignment.
A multilayered feed-forward ANN architecture trained using the error-back-propagation (EBP) algorithm has been developed for predicting whether a given nucleotide sequence is a mycobacterial promoter sequence.
Functionally similar noncoding RNA molecules can be especially difficult to extract from genomics data because structure is more strongly conserved than sequence in RNA as well as in proteins, and the more limited alphabet of RNA decreases the information content of any given nucleotide at any given position.
A minority SNP was defined as present if occurring ≥25% of the time at a given nucleotide position.
The overall mean recombination rate was 5.4×10−4 per locus, with any given nucleotide being about 15 times more likely to be changed by mutation as by recombination (see Table S4).
In the exponential distribution <img src="http://journals.plos.org/plosone/article/asset?id=info?doi/10.1371/journal.pone.0006456.e015.PNG" class= inline-graphic"/> is the probability that a given nucleotide triplet is a stop codon [ 23], [ 24].
Y. pestis had among the highest average coverage (i.e. the number of reads that represent any given nucleotide) and number of INDELs, but all genomes contained potential 454-introduced errors.
The minimum z-score across three spot replicates on each of two array replicates for each sample was taken as the significance score for a given nucleotide and position.
Moreover, for the case of dinucleotides, we also examine the significance of the ratio of the frequency of a dinucleotide over its expected value given nucleotide content, which we refer to as the η statistic, by the same procedure.
The net consequence of recombination, which is measured by the rate at which a given nucleotide is substituted by recombination versus point mutation (r/m), demonstrates that a change is almost twice as likely to be produced by recombination in the ST31 complex and its triple-locus variants than in ST10 and triple locus variants (Table 1).
We used as measure of evolutionary conservation the phastCons score [54] representing the probability that a given nucleotide is part of a block of conservation, given the genome alignments of a number of placental mammals (human, chimpanzee, rhesus monkey, bush baby, treeshrew, rat, mouse, guinea pig, rabbit, shrew, hedgehog, dog, cat, horse, cow, armadillo, elephant and tenrec).
