Alternative splicing can produce variant proteins and expression patterns as different the products of genes, yet prevalence alternative has not been quantified. Here spliced alignment algorithm was used to make a first inventory exon-intron structures known human genes using EST contigs from TIGR Human Gene Index. The results on any one gene may be incomplete will require verification, overall trends are significant. Evidence shown in 35% majority events occurred 5′ untranslated regions,...

Using comparative analysis of genes, operons, and regulatory elements, we describe the cobalamin (vitamin B12) biosynthetic pathway in available prokaryotic genomes. Here found a highly conserved RNA secondary structure, B12 element, which is widely distributed upstream regions biosynthetic/transport genes eubacteria. In addition, binding signal (CBL-box) for hypothetical regulator was identified some archaea. A search elements CBL-boxes positional large number new candidate B12-regulated...

Vitamin B₁ in its active form thiamin pyrophosphate is an essential coenzyme that synthesized by coupling of pyrimidine (hydroxymethylpyrimidine; HMP) and thiazole (hydroxyethylthiazole) moieties bacteria. Using comparative analysis genes, operons, regulatory elements, we describe the biosynthetic pathway available bacterial genomes. The previously detected thiamin-regulatory element,<i>thi</i> box (Miranda-Rios, J., Navarro, M., Soberon, M. (2001) <i>Proc. Natl. Acad. Sci. U. S....

Gene recognition is one of the most important problems in computational molecular biology. Previous attempts to solve this problem were based on statistics, and applications combinatorial methods for gene almost unexplored. Recent advances large-scale cDNA sequencing open a way toward new approach that uses previously sequenced genes as clue newly genes. This paper describes spliced alignment algorithm software tool explores all possible exon assemblies polynomial time finds multiexon...

Zinc is an important component of many proteins, but in large concentrations it poisonous to the cell. Thus its transport regulated by zinc repressors ZUR proteobacteria and Gram-positive bacteria from Bacillus group AdcR Streptococcus group. Comparative computational analysis allowed us identify binding signals GAAATGTTATA N TATAACATTTC for γ-proteobacteria, GTAATGTA AT AACATTAC Agrobacterium group, GATATGTT AACATATC Rhododoccus TAAATCGTAAT ATTACGATTTA bacteria, TTAAC YR GTTAA streptococcal...

Cobalamin in the form of adenosylcobalamin (Ado-CBL) is known to repress expression genes for vitamin B(12) biosynthesis and be transported by a posttranscriptional regulatory mechanism, which involves direct binding Ado-CBL 5'untranslated gene regions (5'UTR). Using comparative analysis regions, we identified highly conserved RNA structure, B12-element, widely distributed 5'UTRs B(12)-related eubacteria. Multiple alignment approximately 200 B12-elements from 66 bacterial genomes reveals...

Intragenomic and intergenomic comparisons of upstream nucleotide sequences archaeal genes were performed with the goal predicting transcription regulatory sites (operators) identifying likely regulons. Learning sets for detection constructed using available experimental data on regulation or by analogy known bacterial regulons, further analysis was iterative profile searches. The information content candidate signals detected this method is insufficient reliable predictions to be made....

Recognition of transcription regulation sites (operators) is a hard problem in computational molecular biology. In most cases, small sample size and low degree sequence conservation preclude the construction reliable recognition rules. We suggest an approach to this based on simultaneous analysis several related genomes. It appears that as long gene coding for regulator conserved compared bacterial genomes, respective group genes (regulons) also tends be maintained. Thus can confidently...

Abstract The increasing volume of genomic data opens new possibilities for analysis protein function. We introduce a method automated selection residues that determine the functional specificity proteins with common general function (the specificity‐determining positions [SDP] prediction method). Such are assumed to be conserved within groups orthologs (that may have same specificity) and vary between paralogs. Thus, considering multiple sequence alignment family divided into orthologous...

Yield of protein per translated mRNA may vary by four orders magnitude. Many studies analyzed the influence features on translation yield. However, a detailed understanding how sequence determines its propensity to be is still missing. Here, we constructed set reporter plasmid libraries encoding CER fluorescent preceded randomized 5΄ untranslated regions (5΄-UTR) and Red (RFP) used as an internal control. Each library was transformed into Escherchia coli cells, separated efficiency cell...

Abstract The ability of nucleic acids to form double-stranded structures is essential for all living systems on Earth. Current knowledge functional RNA focused locally-occurring base pairs. However, crosslinking and proximity ligation experiments demonstrated that long-range are highly abundant. Here, we present the most complete to-date catalog conserved complementary regions (PCCRs) in human protein-coding genes. PCCRs tend occur within introns, suppress intervening exons, obstruct cryptic...

Eukaryotic gene expression is regulated post-transcriptionally by a mechanism called unproductive splicing, in which mRNA triggered to degrade the nonsense-mediated decay (NMD) pathway as result of alternative splicing (AS). Only few dozen events (USEs) are currently documented, and many more remain be identified. Here, we analyzed RNA-seq experiments from Genotype-Tissue Expression (GTEx) Consortium identify USEs, an increase NMD isoform rate accompanied tissue-specific down-regulation host...

SDPpred (Specificity Determining Position prediction) is a tool for prediction of residues in protein sequences that determine the proteins' functional specificity. It designed analysis families whose members have biochemically similar but not identical interaction partners (e.g. different substrates family transporters). predicts could be responsible choice their correct partners. The input multiple alignment divided into number specificity groups, within which partner believed to same....

The tumor-associated ganglioside GD2 represents an attractive target for cancer immunotherapy. GD2-positive tumors are more responsive to such targeted therapy, and new methods needed the screening of molecular tumor phenotypes. In this work, we built a gene expression-based binary classifier predicting To end, compared RNA sequencing data from human biopsy material experimental samples public databases as well GD2-negative cell lines, expression levels genes encoding enzymes involved in...

Abstract Increasingly many studies reveal how ribosome composition can be tuned to optimally translate the transcriptome of individual cell types. In this study, we investigated expression pattern, structure within and effect on protein synthesis ribosomal paralog 39L (RPL39L). With a novel mass spectrometric approach revealed RPL39L beyond mouse germ cells, in human pluripotent cancer lines tissue samples. We generated knock-out embryonic stem (mESC) demonstrated that impacts dynamics...

Comparative analysis of alternative splicing orthologous genes from fruit flies ( Drosophila melanogaster and pseudoobscura ) mosquito Anopheles gambiae demonstrated that both in the fly fly–mosquito comparisons, constitutive exons sites are more conserved than ones. While &gt;97% D. pseudoobscura, only ∼80% conserved. Similarly, 77% genes, compared with &lt;50% exons. Internal alternatives terminal Retained introns least conserved, acceptor slightly donor sites, mutually exclusive almost as...

A new approach has been proposed for predicting the kinetic ensemble of RNA secondary structures during chain growth. It is based on an analysis time intervals in structural reconstruction. The Markov employed describing reconstruction was modelled Monte Carlo method. calculation made possible formed transcription. An algorithm also suggested search a helix with bulge type defect which cooperative effect retained. Kinetic ensembles SD-sites and initiation regions polycistronic mRNA...

<ns3:p>Background RNA sequencing (RNA-seq) is a widely used technique in many scientific studies. Given the plethora of models and software packages that have been developed for processing analyzing RNA-seq datasets, choosing most appropriate ones time-consuming process requires an in-depth understanding data, as well principles parameters each tool. In addition, designed individual tasks are different programming languages dependencies various degrees complexity, which renders their...

Tandem alternative splice sites (TASS) is a special class of splicing events that are characterized by close tandem arrangement sites. Most TASS lack functional characterization and believed to arise from noise. Based on the RNA-seq data Genotype Tissue Expression project, we present an extended catalogue in healthy human tissues analyze their tissue-specific expression. The expression usually dominated one major site (maSS), while minor (miSS) at least order magnitude lower. Among 46k miSS...

Splice sites (SSs)—short nucleotide sequences flanking introns—are under selection for spliceosome binding, and adhere to consensus sequences. However, non-consensus nucleotides, many of which probably reduce SS performance, are frequent. Little is known about the mechanisms maintaining such apparently suboptimal SSs. Here, we study correlations between strengths nucleotides occupying different positions same SS. Such may arise due epistatic interactions (i.e., a situation when fitness...

Abstract Background The origin of the selective nuclear protein import machinery, which consists pore complexes and adaptor molecules interacting with localization signals (NLSs) cargo molecules, is one most important events in evolution eukaryotic cells. How proteins were selected for into forming nucleus remains an open question. Results Here, we demonstrate that functional NLSs may be integrated nucleotide-binding domains both prokaryotic coevolve these domains. Conclusion presence...