This paper presents the utilization of progressive alignment principle for positional adjustment of a set of genomic signals with different lengths. The new method of multiple alignment of signals based on dynamic time warping is tested for the purpose of evaluating the similarity of different length genes in phylogenetic studies. Two sets of phylogenetic markers were used to demonstrate the effectiveness of the evaluation of intraspecies and interspecies genetic variability. The part of the proposed method is modification of pairwise alignment of two signals by dynamic time warping with using correlation in a sliding window. The correlation based dynamic time warping allows more accurate alignment dependent on local homologies in sequences without the need of scoring matrix or evolutionary models, because mutual similarities of residues are included in the numerical code of signals.

• MeSH
• algoritmy MeSH
• bakteriální RNA genetika   MeSH
• druhová specificita MeSH
• fylogeneze MeSH
• genom bakteriální * MeSH
• genomika metody   MeSH
• počítačové zpracování signálu MeSH
• RNA ribozomální 18S genetika   MeSH
• sekvenční seřazení metody   MeSH
• výpočetní biologie metody   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

• MeSH
• genetické markery analýza   MeSH
• molekulární biologie metody   MeSH
• sekvence nukleotidů MeSH
• software MeSH
• technika náhodné amplifikace polymorfní DNA MeSH
• Publikační typ
• kongresy MeSH

• MeSH
• biologické vědy MeSH
• genetika MeSH

• Konspekt
• Obecná genetika. Obecná cytogenetika. Evoluce
• NLK Obory
• genetika, lékařská genetika

• MeSH
• lidé MeSH
• počítačová grafika MeSH
• sekvenční analýza MeSH
• sekvenční seřazení MeSH
• software MeSH
• Check Tag
• lidé MeSH

BACKGROUND: Understanding the architecture and function of RNA molecules requires methods for comparing and analyzing their tertiary and quaternary structures. While structural superposition of short RNAs is achievable in a reasonable time, large structures represent much bigger challenge. Therefore, we have developed a fast and accurate algorithm for RNA pairwise structure superposition called SETTER and implemented it in the SETTER web server. However, though biological relationships can be inferred by a pairwise structure alignment, key features preserved by evolution can be identified only from a multiple structure alignment. Thus, we extended the SETTER algorithm to the alignment of multiple RNA structures and developed the MultiSETTER algorithm. RESULTS: In this paper, we present the updated version of the SETTER web server that implements a user friendly interface to the MultiSETTER algorithm. The server accepts RNA structures either as the list of PDB IDs or as user-defined PDB files. After the superposition is computed, structures are visualized in 3D and several reports and statistics are generated. CONCLUSION: To the best of our knowledge, the MultiSETTER web server is the first publicly available tool for a multiple RNA structure alignment. The MultiSETTER server offers the visual inspection of an alignment in 3D space which may reveal structural and functional relationships not captured by other multiple alignment methods based either on a sequence or on secondary structure motifs.

• MeSH
• algoritmy * MeSH
• internet * MeSH
• konformace nukleové kyseliny * MeSH
• RNA chemie   MeSH
• sekvenční analýza RNA metody   MeSH
• sekvenční seřazení metody   MeSH
• software * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

MOTIVATION: Satellite DNA makes up significant portion of many eukaryotic genomes, yet it is relatively poorly characterized even in extensively sequenced species. This is, in part, due to methodological limitations of traditional methods of satellite repeat analysis, which are based on multiple alignments of monomer sequences. Therefore, we employed an alternative, alignment-free, approach utilizing k-mer frequency statistics, which is in principle more suitable for analyzing large sets of satellite repeat data, including sequence reads from next generation sequencing technologies. RESULTS: k-mer frequency spectra were determined for two sets of rice centromeric satellite CentO sequences, including 454 reads from ChIP-sequencing of CENH3-bound DNA (7.6 Mb) and the whole genome Sanger sequencing reads (5.8 Mb). k-mer frequencies were used to identify the most conserved sequence regions and to reconstruct consensus sequences of complete monomers. Reconstructed consensus sequences as well as the assessment of overall divergence of k-mer spectra revealed high similarity of the two datasets, suggesting that CentO sequences associated with functional centromeres (CENH3-bound) do not significantly differ from the total population of CentO, which includes both centromeric and pericentromeric repeat arrays. On the other hand, considerable differences were revealed when these methods were used for comparison of CentO populations between individual chromosomes of the rice genome assembly, demonstrating preferential sequence homogenization of the clusters within the same chromosome. k-mer frequencies were also successfully used to identify and characterize smRNAs derived from CentO repeats.

• MeSH
• centromera genetika   MeSH
• chromozomy rostlin genetika   MeSH
• DNA rostlinná genetika   MeSH
• konzervovaná sekvence genetika   MeSH
• molekulární sekvence - údaje MeSH
• rýže (rod) genetika   MeSH
• satelitní DNA genetika   MeSH
• sekvence nukleotidů MeSH
• sekvenční analýza DNA metody   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH

• MeSH
• fyzikální jevy MeSH
• magnetická rezonanční tomografie MeSH

• Konspekt
• Patologie. Klinická medicína
• NLK Obory
• radiologie, nukleární medicína a zobrazovací metody
• NLK Publikační typ
• kolektivní monografie

Among schistosomatids, Trichobilharzia regenti, displays an unusual migration through the peripheral and central nervous system prior to residence in the nasal cavity of the definitive avian host. Migration causes tissue degradation and neuromotor dysfunction both in birds and experimentally infected mice. Although schistosomula have a well-developed gut, the peptidases elaborated that might facilitate nutrition and migration are unknown. This is, in large part, due to the difficulty in isolating large numbers of migrating larvae. We have identified and characterised the major 33 kDa cathepsin B-like cysteine endopeptidase in extracts of migrating schistosomula using fluorogenic peptidyl substrates with high extinction coefficients and irreversible affinity-labels. From first strand schistosomula cDNA, degenerate PCR and Rapid Amplification of cDNA End protocols were used to identify peptidase isoforms termed TrCB1.1-TrCB1.6. Highest sequence homology is to the described Schistosoma mansoni and Schistosoma japonicum cathepsins B1. Two isoforms (TrCB1.5 and 1.6) encode putatively inactive enzymes as the catalytic cysteine is substituted by glycine. Two other isoforms, TrCB1.1 and 1.4, were functionally expressed as zymogens in Pichia pastoris. Specific polyclonal antibodies localised the peptidases exclusively in the gut of schistosomula and reacted with a 33kDa protein in worm extracts. TrCB1.1 zymogen was unable to catalyse its own activation, but was trans-processed and activated by S. mansoni asparaginyl endopeptidase (SmAE aka. S. mansoni legumain). In contrast, TrCB1.4 zymogen auto-activated, but was resistant to the action of SmAE. Both activated isoforms displayed different pH-dependent specificity profiles with peptidyl substrates. Also, both isoforms degraded myelin basic protein, the major protein component of nervous tissue, but were inefficient against hemoglobin, thus supporting the adaptation of T. regenti gut peptidases to parasitism of host nervous tissue.

• MeSH
• cysteinové endopeptidasy metabolismus   MeSH
• encefalitogenní základní proteiny metabolismus   MeSH
• financování organizované MeSH
• genetická transkripce MeSH
• imunohistochemie metody   MeSH
• infekce červy třídy Trematoda metabolismus   MeSH
• isomerie MeSH
• kathepsin B analýza   chemie   MeSH
• messenger RNA genetika   MeSH
• molekulární modely MeSH
• molekulární sekvence - údaje MeSH
• prekurzory enzymů analýza   MeSH
• rekombinantní proteiny analýza   MeSH
• RNA helmintů genetika   MeSH
• Schistosomatidae genetika   chemie   MeSH
• sekvence nukleotidů MeSH
• sekvenční seřazení mortalita   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH

Various sources of protein data, such as knowledgebases and scientific literature, are currently available, as are numerous tools for their analysis. The matter becomes one of choosing the tools that are most appropriate for the specific task and for the specific proteins. A combination of standard and alternative tools may lead to biologically significant results. Here, a computational classification of proteins is made using standard multiple sequence alignment in combination with an alternative method for analysis of hydropathy distribution in proteins. Both of these methods are applied to the Na+/Cl--dependent neurotransmitter symporters (NSSs), resulting in two alternative classifications. The classifications are validated and interpreted biologically by literature and knowledgebase annotation mining, producing a consensus classification. The classification leads to the identification and functional characterization of three families of largely structurally and functionally uncharacterized orphan NSSs. The literature and knowledgebase annotations are mined to functionally characterize the NSSs in these families. The presented work also demonstrates that, in specific cases, the analysis of the hydropathy distribution in proteins is capable of revealing functional properties of proteins.

• MeSH
• databáze proteinů MeSH
• financování organizované MeSH
• hydrofobní a hydrofilní interakce MeSH
• mapování interakce mezi proteiny klasifikace   MeSH
• proteiny přenášející neurotransmitery přes plazmatickou membránu klasifikace   metabolismus   MeSH
• sekvenční analýza proteinů metody   MeSH
• sekvenční seřazení MeSH
• výpočetní biologie metody   MeSH
• znalostní báze MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• srovnávací studie MeSH
• validační studie MeSH

• MeSH
• sekvence nukleotidů metody   MeSH
• sekvenční analýza proteinů metody   MeSH
• výpočetní biologie metody   MeSH

• Konspekt
• Biochemie. Molekulární biologie. Biofyzika
• NLK Obory
• biochemie