PMC

Example of reference in a prefix trie, query in prefix DAWG, and the suffix array of the input string “BANANA$”. (a) represents reference prefix trie searching for any substring of the string by staring at the root and following matches down the tree until being exhausted. (b) represents prefix DAWG constructed by collapsing nodes with the identical suffix array interval. DAWG transformed from the prefix trie of the query sequence. (c) represents a constructed string suffix automaton (DAWG). (d) represents the suffix array for string “BANANA$”. The dollar sign $ is a regular expression that denotes the end of a line in the reference sequence.

The chemokine receptor gene family in two teleost species. (A) Phylogenetic tree based on derived protein sequences of chemokine receptor genes of human (prefix Hs), mouse (prefix Mm), medaka (prefix Ol), and tetraodon (prefix Tn) genomes. The sequence for the human formyl-peptide receptor FPR1 was used as an outgroup. (B) Expression of chemokine receptor genes in medaka from 5 dpf until larval stage. White box indicates no expression, filled box indicates expression detected by WISH.

Images of silver-stained analytical 2D protein gels from (A) E15 and (B) P8 ovaries. The prefix D indicates downregulated protein spots, prefix B indicates upregulated protein spots, prefix N indicates newly appeared protein spots, and prefix H indicates unchanged protein spots. Broken white circles highlight the area of the protein spots, some of which are intense while other are faint. These gel images were used as templates to retrieve protein spots from SyproRuby stained preparative gels. (C) The percentage of protein spots in various categories. L, landmarks used for gel alignment.

The dendrogram of normal samples from Oncobox (no prefix in sample names), TCGA database (“TCGA_” prefix in samples names) and ENCODE (“ENCODE_” prefix in samples names). For the TCGA data 10 random samples per tissue type were selected for visualization, in cases when more norms were available. Euclidian distance between the samples was measured using gene expression data. The dendrogram was built using R ward.D2 method. The color markers indicate the tissue type. The lower scales indicate the number of uniquely mapped reads.