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Background: This study seeks to develop, test and assess a methodology for automatic extraction of a complete set of 'term-like phrases' and to create a terminology spectrum from a collection of natural language PDF documents in the field of chemistry. The definition of 'term-like phrases' is one or more consecutive words and/or alphanumeric string combinations with unchanged spelling which convey specific scientific meanings. A terminology spectrum for a natural language document is an indexed list of tagged entities including: recognized general scientific concepts, terms linked to existing thesauri, names of chemical substances/reactions and term-like phrases. The retrieval routine is based on n-gram textual analysis with a sequential execution of various 'accept and reject' rules with taking into account the morphological and structural information., Results: The assessment of the retrieval process, expressed quantitatively with a precision (P), recall (R) and F1-measure, which are calculated manually from a limited set of documents (the full set of text abstracts belonging to 5 EuropaCat events were processed) by professional chemical scientists, has proved the effectiveness of the developed approach. The term-like phrase parsing efficiency is quantified with precision (P = 0.53), recall (R = 0.71) and F1-measure (F1 = 0.61) values., Conclusion: The paper suggests using such terminology spectra to perform various types of textual analysis across document collections. This sort of the terminology spectrum may be successfully employed for text information retrieval, for reference database development, to analyze research trends in subject fields of research and to look for the similarity between documents.Graphical abstractTerminology spectrum building process with term-like phrases retrieval.

Divergence patterns of the banding sequences from the chromosomal arms A, C, D, E, and F were compared in 63 species of the genus Chironomus. Evaluation of the number of breakpoints between the pairs of inverted banding sequences and the analysis of the lengths of the conserved segments in the chromosomal arms in the chironomid species examined showed that different arms evolved relatively independently and at different rates. No direct correlation between the arm length and the breakpoints number was observed. The length of the conservative segment was not fixed, but was arm-specific. Robustness and fidelity of the estimates of phylogenetic relationships between the species examined increased with the arm number, i.e., with the genome proportion included in the analysis.

Banding sequences of five chromosomal arms (A, C, D, E, and F), accounting for about 70% of the total genome size in 63 Chironomus species, were used as phylogenetic markers to analyze divergence patterns of the linear genome structure during the evolution. The number of chromosomal breakpoints between the pairs of banding sequences compared served as a measure of divergence. It was demonstrated that the greater the divergence between the species compared, the higher the number of chromosomal breakpoints and the smaller the size of the conserved chromosomal regions. A banding sequences comparison in sibling species demonstrated a lower number of chromosomal breakpoints; the breakpoint number was maximum in a comparison of the banding sequences in the subgenera Chironomus and Camptochironomus. The use of the number of chromosomal breakpoints as a divergence measure provided establishment of phylogenetic relationships between 63 Chironomus species and discrimination of sibling species groups and cytocomplexes on a phylogenetic tree.

Complexity analysis is capable of highlighting those gross evolutionary changes in gene promoter regions (loosely termed "promoter shuffling") that are undetectable by conventional DNA sequence alignment. Complexity analysis was therefore used here to identify the modular components (blocks) of the orthologous beta-globin gene promoter sequences of 22 vertebrate species, from zebrafish to humans. Considerable variation between the beta-globin gene promoters was apparent in terms of block presence/absence, copy number, and relative location. Some sequence blocks appear to be ubiquitous, whereas others are restricted to a specific taxon. Block similarities were also evident between the promoters of the paralogous human beta-like globin genes. It may be inferred that a wide variety of different mutational mechanisms have operated upon the beta-globin gene promoter over evolutionary time. Because these include gross changes such as deletion, duplication, amplification, elongation, contraction, and fusion, as well as the steady accumulation of single base-pair substitutions, it is clear that some redefinition of the term "promoter shuffling" is required. This notwithstanding, and as previously described for the vertebrate growth hormone gene promoter, the modular structure of the beta-globin promoter region and those of its paralogous counterparts have continually been rearranged into new combinations through the alteration, or shuffling, of preexisting blocks. Some of these changes may have had no influence on promoter function, but others could have altered either the level of gene expression or the responsiveness of the promoter to external stimuli. The comparative study of vertebrate beta-globin gene promoter regions described here confirms the generality of the phenomenon of sequence block shuffling and thus supports the view that it could have played an important role in the evolution of differential gene expression.

It is now common practice to retrieve, by key words, highly specialized selections of sequences from general-purpose databases such as EMBL, GenBank, etc. The sequences included in a selection are often interconnected, which means that there are duplications, embeddings, intersections, homology, common structural elements. Knowledge of these interconnections is necessary for further processing of the sequences. We propose a rapid (single scan) method for identification of such interconnections by means of complexity analysis that generalizes the Lempel-Ziv approach. Analysis of a selection of 5'-flanking regions of vertebrate growth hormone genes from EMBL is presented as an example.

Comparative studies of vertebrate gene promoter regions seldom detect gross rearrangements ('promoter shuffling') since such analyses usually employ relatively similar DNA sequences. Conversely, attempts to compare evolutionarily more divergent promoter sequences have been largely unsuccessful owing to the inability of conventional alignment procedures to deal with gross rearrangements. These limitations have been circumvented in the present study by using the novel technique of complexity analysis to identify modular components ('blocks') in the growth hormone (GH) gene promoter sequences of some 22 vertebrate species, from salmon to human. Significant rearrangement of blocks was found to have occurred, indicating that they have evolved as independent units. Some blocks appear to be ubiquitous, whereas others are restricted to a specific taxon. Considerable variation between orthologous GH gene promoters was apparent in terms of block length, copy number and relative location. It may be inferred that a wide variety of different mutational mechanisms have operated upon the GH gene promoter over evolutionary time. These include gross changes such as deletion, duplication, amplification, elongation, contraction, transposition, inversion and fusion, as well as the slow, steady accumulation of single base-pair substitutions. Thus the patchwork structure of the modular GH promoter region, and those of its paralogous GH2 and prolactin (PRL) counterparts, have continually been shuffled into new combinations through the rearrangement of pre-existing blocks. Although some of these changes may have had no influence on promoter function, others could have served to alter either the level of gene expression or the responsiveness of the promoter to external stimuli.

Motivation: It is well known that the regulatory regions of genomes are highly repetitive. They are rich in direct, symmetric and complemented repeats, and there is no doubt about the functional significance of these repeats. Among known measures of complexity, the Ziv-Lempel complexity measure reflects most adequately repeats occurring in the text. But this measure does not take into account isomorphic repeats. By isomorphic repeats we mean fragments that are identical (or symmetric) modulo some permutation of the alphabet letters., Results: In this paper, two complexity measures of symbolic sequences are proposed that generalize the Ziv-Lempel complexity measure by taking into account any isomorphic repeats in the text (rather than just direct repeats as in Ziv-Lempel). The first of them, the complexity vector, is designed for small alphabets such as the alphabet of nucleotides. The second is based on a search for the longest isomorphic fragment in the history of sequence synthesis and can be used for alphabets of arbitrary cardinality. These measures have been used for recognition of structural regularities in DNA sequences. Some interesting structures related to the regulatory region of the human growth hormone are reported.

The suggested earlier complexity approach for detecting structural regularities in primary structures of nucleic acids is illustrated by using lambda phage as an example. Among the most interesting regularities detected in the lambda phage genome are the following: (a) the presence of "extended homology zones" i.e. fragments in which block transpositions of duplicative type predominate explicitly; (b) the abundance of palindrome-hairpin structures and duplications in the origins and termini of many genes; (c) the hierarchy in the repeats and inversions organization.

A new computer method for detecting local structural regularities in genomes of different microorganisms is described. The method is based on the concepts of complexity and complexity profile of a finite sequence. The complexity measure taking into account the specificity of genetic texts (presence of repeats, symmetries, inversions) is proposed. The genomes of different viruses and bacteriophages contained in Genbank were processed. The classification and interpretation of structural regularities were carried out.