Multiple alignment

In this paper an approach devised to perform multiple alignment is described, able to exploit any available secondary structure information. In particular, given the sequences to be aligned, their secondary structure (either available or predicted) is used to perform an ...

Mitochondria, besides their central role in energy metabolism, have recently been found to be involved in a number of basic processes of cell life and to contribute to the pathogenesis of many degenerative diseases. All functions of mitochondria depend on the interaction of nuclear and organellar genomes. Mitochondrial genomes have been extensively sequenced and analysed and the data collected in several specialised databases. In order to collect information on nuclear coded mitochondrial proteins we developed MitoNuc and MitoAln, two related databases containing, respectively, detailed information on sequenced nuclear genes coding for mitochondrial proteins in Metazoa and yeast, and the multiple alignments of the relevant homologous protein coding regions. MitoNuc and MitoAln retrieval through SRS at http://bio-www.ba.cnr.it:8000/srs6/ can easily allow the extraction of sequence data, subsequences defined by specific features and nucleotide or amino acid multiple alignments.

The pyridine nucleotide cycle is a network of salvage and recycling routes maintaining homeostasis of NAD(P) cofactor pool in the cell. Nicotinamide mononucleotide (NMN) deamidase (EC 3.5.1.42), one of the key enzymes of the bacterial pyridine nucleotide cycle, was originally described in Enterobacteria, but the corresponding gene eluded identification for over 30 years. A genomics-based reconstruction of NAD metabolism across hundreds of bacterial species suggested that NMN deamidase reaction is the only possible way of nicotinamide salvage in the marine bacterium Shewanella oneidensis. This prediction was verified via purification of native NMN deamidase from S. oneidensis followed by the identification of the respective gene, termed pncC. Enzymatic characterization of the PncC protein, as well as phenotype analysis of deletion mutants, confirmed its proposed biochemical and physiological function in S. oneidensis. Of the three PncC homologs present in Escherichia coli, NMN deamidase activity was confirmed only for the recombinant purified product of the ygaD gene. A comparative analysis at the level of sequence and three-dimensional structure, which is available for one of the PncC family member, shows no homology with any previously described amidohydrolases. Multiple alignment analysis of functional and nonfunctional PncC homologs, together with NMN docking experiments, allowed us to tentatively identify the active site area and conserved residues therein. An observed broad phylogenomic distribution of predicted functional PncCs in the bacterial kingdom is consistent with a possible role in detoxification of NMN, resulting from NAD utilization by DNA ligase.

Multiple Alignment is a new interface for performing and analyzing multiple protein structure alignments. It enables viewing levels of sequence and structure similarity on the aligned structures and performing a variety of evolutionary and bioinformatic tasks, including the construction of structure-based phylogenetic trees and minimal basis sets of structures that best represent the topology of the phylogenetic tree. It is implemented as a plugin for VMD (Visual Molecular Dynamics), which is distributed by the NIH Resource for Macromolecular Modeling and Bioinformatics at the University of Illinois.

Bounds are given on the size of the parameter-space decomposition induced by multiple sequence alignment problems where phylogenetic information may be given or inferred. It is shown that many of the usual formulations of these problems fall within the same integer parametric framework, implying that the number of distinct optima obtained as the parameters are varied across their ranges is polynomially bounded in the length and number of sequences.

The PLHC-1 hepatoma cell line derived from topminnow (Poeciliopsis lucida) is one of the most frequently used fish cell lines in aquatic ecotoxicology. These cells have been well characterized regarding the presence of phase I and phase II enzymes involved in the metabolism of xenobiotics. However, the presence of the ABC transport proteins possibly involved in the MultiXenobiotic Resistance (MXR) mechanism as phase III of cellular detoxification has never been described in the PLHC-1 cells. The main goal of this study was the detection and functional characterization of toxicologically relevant xenobiotic efflux transporters from ABCB and ABCC subfamily in the PLHC-1 cells. Using specific primer pairs two PCR products 1769 and 1023 bp in length were successfully cloned and sequenced. Subsequent multiple alignment and phylogenetic analysis showed that these sequences share a high degree of homology with the P-glycoprotein (Pgp1; ABCB1) and the MRP3 (ABCC3). Functional experiments with fluorescent model substrates and specific inhibitors were used to verify that transport activities of Pgp-and MRP-related proteins are indeed present in PLHC-1 cells. Accumulation or efflux/retention rates of rhodamine 123, calcein-AM or monochlorbimane were time-and concentration-dependent. Cyclosporine A, MK571, verapamil, reversine 205, indomethacine and probenecid were used as specific inhibitors of Pgp1 and/or MRPs transport activities, resulting in a dose dependent inhibition of related transport activities in PLHC-1 cells. Similar to mammalian systems, the obtained IC 50 values were in the lower micromolar range. Taken together these data demonstrate that: (1) the PLHC-1 cells do express a functional MXR mechanism mediated by toxicologically relevant ABC efflux transporters; and (2) the presence of all three critical phases of cellular detoxification additionally affirms the PLHC-1 cells as a reliable in vitro model in aquatic toxicology.

Multiple sequence alignment is one of the important research topics of bioinformatics. The objective is to maximize the similarities between them by adding and shuffling gaps. We propose a hybrid algorithm based on genetic (GAs) and 2-optimal algorithms. We are using permutation coding corresponding to represent the solution, and we are studying scoring function for multiple alignments, that is used

ABSTRACTThe metallo-β-lactamases fall into two groups: Ambler class B subgroups B1 and B2 and Ambler class B subgroup B3. The two groups are so distantly related that there is no detectable sequence homology between members of the two different groups, but homology is clearly detectable at the protein structure level. The multiple structure alignment program MAPS has been used to align the structures of eight metallo-β-lactamases and five structurally homologous proteins from the metallo-β-lactamase superfamily, and that alignment has been used to construct a phylogenetic tree of the metallo-β-lactamases. The presence of genes fromEubacteria,Archaebacteria, andEukaryotaon that tree is consistent with a very ancient origin of the metallo-β-lactamase family.

We present a profile-profile multiple alignment strategy that uses database searching to collect homologues for each sequence in a given set, in order to enrich their available evolutionary information for the alignment. For each of the alignment sequences, the putative homologous sequences that score above a pre-defined threshold are incorporated into a position-specific pre-alignment profile. The enriched position-specific profile is used for standard progressive alignment, thereby more accurately describing the characteristic features of the given sequence set. We show that owing to the incorporation of the pre-alignment information into a standard progressive multiple alignment routine, the alignment quality between distant sequences increases significantly and outperforms state-of-the-art methods, such as T-COFFEE and MUSCLE. We also show that although entirely sequence-based, our novel strategy is better at aligning distant sequences when compared with a recent contact-based alignment method. Therefore, our pre-alignment profile strategy should be advantageous for applications that rely on high alignment accuracy such as local structure prediction, comparative modelling and threading.

Background: A long term research goal of venomics, of applied importance for improving current antivenom therapy, but also for drug discovery, is to understand the pharmacological potential of venoms. Individually or combined, proteomic and transcriptomic studies have demonstrated their feasibility to explore in depth the molecular diversity of venoms. In the absence of genome sequence, transcriptomes represent also valuable searchable databases for proteomic projects. Results: The venom gland transcriptomes of 8 Costa Rican taxa from 5 genera (Crotalus, Bothrops, Atropoides, Cerrophidion, and Bothriechis) of pitvipers were investigated using high-throughput 454 pyrosequencing. 100,394 out of 330,010 masked reads produced significant hits in the available databases. 5.165,220 nucleotides (8.27%) were masked by RepeatMasker, the vast majority of which corresponding to class I (retroelements) and class II (DNA transposons) mobile elements. BLAST hits included 79,991 matches to entries of the taxonomic suborder Serpentes, of which 62,433 displayed similarity to documented venom proteins. Strong discrepancies between the transcriptome-computed and the proteome-gathered toxin compositions were obvious at first sight. Although the reasons underlaying this discrepancy are elusive, since no clear trend within or between species is apparent, the data indicate that individual mRNA species may be translationally controlled in a species-dependent manner. The minimum number of genes from each toxin family transcribed into the venom gland transcriptome of each species was calculated from multiple alignments of reads matched to a full-length reference sequence of each toxin family. Reads encoding ORF regions of Kazal-type inhibitor-like proteins were uniquely found in Bothriechis schlegelii and B. lateralis transcriptomes, suggesting a genus-specific recruitment event during the early-Middle Miocene. A transcriptome-based cladogram supports the large divergence between A. mexicanus and A. picadoi, and a closer kinship between A. mexicanus and C. godmani. Conclusions: Our comparative next-generation sequencing (NGS) analysis reveals taxon-specific trends governing the formulation of the venom arsenal. Knowledge of the venom proteome provides hints on the translation efficiency of toxin-coding transcripts, contributing thereby to a more accurate interpretation of the transcriptome. The application of NGS to the analysis of snake venom transcriptomes, may represent the tool for opening the door to systems venomics.

Analysis of protein-ligand complexes and recognition of spatially conserved physico-chemical properties is important for the prediction of binding and function. Here, we present two webservers for multiple alignment and recognition of binding patterns shared by a set of protein structures. The first webserver, MultiBind ( MultiBind), performs multiple alignment of protein binding sites. It recognizes the common spatial chemical binding patterns even in the absence of similarity of the sequences or the folds of the compared proteins. The input to the MultiBind server is a set of protein-binding sites defined by interactions with small molecules. The output is a detailed list of the shared physico-chemical binding site properties. The second webserver, MAPPIS (), aims to analyze protein-protein interactions. It performs multiple alignment of protein-protein interfaces (PPIs), which are regions of interaction between two protein molecules. MAPPIS recognizes the spatially conserved physico-chemical interactions, which often involve energetically important hot-spot residues that are crucial for protein-protein associations. The input to the MAPPIS server is a set of protein-protein complexes. The output is a detailed list of the shared interaction properties of the interfaces.

This paper describes the complete structure and partial sequence of the gene encoding diapause protein 1, an arylphorin-type storage hexamer of the Colorado potato beetle, Leptinotarsa decemlineata. This gene contains four introns of variable lengths, the positions of which have been determined accurately. Three of the five exons of the gene are very similar in size to those reported for storage hexamer genes from Lepidoptera. The last two exons differ significantly in size from those found for other storage protein genes. The complete gene for diapause protein 1 encompasses about 9 kb of genomic DNA. The gene encodes a pre-protein of 702 amino acids, including a signal peptide of 17 amino acids. Transcription starts 32 bp upstream from the translation initiation codon. A typical TATA-box is located 27 bp upstream from the transcription initiation site. Multiple alignment analysis of the amino acid sequence reveals extensive homology with storage hexamers from Lepidoptera. This is the first published complete nucleotide and amino acid sequence of a Coleopteran arylphorin. A simple and rapid method is described for mapping the number, size and positions of introns in genomic DNA fragments using PCR. Colorado potato beetle Diapause protein Gene structure DNA sequence Coleopteran arylphorin

Single-nucleotide polymorphisms (SNPs) are the most abundant form of human genetic variation and a resource for mapping complex genetic traits 1. The large volume of data produced by high-throughput sequencing projects is a rich and largely untapped source of SNPs (refs 2-5). We present here a unified approach to the discovery of variations in genetic sequence data of arbitrary DNA sources. We propose to use the rapidly emerging genomic sequence 6,7 as a template on which to layer often unmapped, fragmentary sequence data 8-11 and to use base quality values 12 to discern true allelic variations from sequencing errors. By taking advantage of the genomic sequence we are able to use simpler yet more accurate methods for sequence organization: fragment clustering, paralogue identification and multiple alignment. We analyse these sequences with a novel, Bayesian inference engine, POLY-BAYES, to calculate the probability that a given site is polymorphic. Rigorous treatment of base quality permits completely automated evaluation of the full length of all sequences, without limitations on alignment depth. We demonstrate this approach by accurate SNP predictions in human ESTs aligned to finished and working-draft quality genomic sequences, a data set representative of the typical challenges of sequence-based SNP discovery.

Gene prospection is one of the current challenges for science. Molecular biologists and Bioinformatics need to analyze a large amount of information. Gene prospection still constitutes an area to be explored, mainly in eukaryotes. It involves the combination of bioinformatics, with in silico analyses, and molecular biology with the construction and screening of cDNA libraries. The strategy of gene prospection begins with the construction of cDNA libraries, followed by a search for homology in public databases. Soon afterwards, conserved regions are identified on the selected sequences, throughout multiple alignments. With this information, degenerate primers may be constructed for cDNA screening, which are analyzed to screen one or more genes, using labeled probes or DNA amplification by PCR. The spectacular progress of bioinformatic in the last few years, and the growing computational capacity and speed access on the Internet, helped to accomplish new analyses. The development of m...

Previously published phylogenetic trees reconstructed on ''Rieske protein'' sequences frequently are at odds with each other, with those of other subunits of the parent enzymes and with small-subunit rRNA trees. These differences are shown to be at least partially if not completely due to problems in the reconstruction procedures. A major source of erroneous Rieske protein trees lies in the presence of a large, poorly conserved domain prone to accommodate very long insertions in well-defined structural hot spots substantially hampering multiple alignments. The remaining smaller domain, in contrast, is too conserved to allow distant phylogenies to be deduced with sufficient confidence. Three-dimensional structures of representatives from this protein family are now available from phylogenetically distant species and from diverse enzymes. Multiple alignments can thus be refined on the basis of these structures. We show that structurally guided alignments of Rieske proteins from Rieske-cytochrome b complexes and arsenite oxidases strongly reduce conflicts between resulting trees and those obtained on their companion enzyme subunits. Further problems encountered during this work, mainly consisting in database errors such as wrong annotations and frameshifts, are described. The obtained results are discussed against the background of hypotheses stipulating pervasive lateral gene transfer in prokaryotes.

We present a new algorithm, based on the multidimensional QR factorization, to remove redundancy from a multiple structural alignment by choosing representative protein structures that best preserve the phylogenetic tree topology of the homologous group. The classical QR factorization with pivoting, developed as a fast numerical solution to eigenvalue and linear least-squares problems of the form AxZb, was designed to

We use a quantitative definition of specificity to develop a neural network for the identification of common protein binding sites in a collection of unaligned DNA fragments. We demonstrate the equivalence of the method to maximizing Information Content of the aligned sites when simple models of the binding energy and the genome are employed. The network method subsumes those simple models and is capable of working with more complicated ones. This is demonstrated using a Markov model of the E. coli genome and a sampling method to approximate the partition function. A variation of Gibbs' sampling aids in avoiding local minima.

Since the publication of the first draft of the human genome in 2000, bioinformatic data have been accumulating at an overwhelming pace. Currently, more than 3 million sequences and 35 thousand structures of proteins and nucleic acids are available in public databases. Finding correlations in and between these data to answer critical research questions is extremely challenging. This problem needs to be approached from several directions: information science to organize and search the data; information visualization to assist in recognizing correlations; mathematics to formulate statistical inferences; and biology to analyze chemical and physical properties in terms of sequence and structure changes. Here we present MultiSeq, a unified bioinformatics analysis environment that allows one to organize, display, align and analyze both sequence and structure data for proteins and nucleic acids. While special emphasis is placed on analyzing the data within the framework of evolutionary bio...

Conserved segments in DNA or protein sequences are strong candidates for functional elements and thus appropriate methods for computing them need to be developed and compared. We describe five methods and computer programs for finding highly conserved blocks within previously computed multiple alignments, primarily for DNA sequences. Two of the methods are already in common use; these are based on good column agreement and high information content. Three additional methods find blocks with minimal evolutionary change, blocks that differ in at most k positions per row from a known center sequence and blocks that differ in at most k positions per row from a center sequence that is unknown a priori. The center sequence in the latter two methods is a way to model potential binding sites for known or unknown proteins in DNA sequences. The efficacy of each method was evaluated by analysis of three extensively analyzed regulatory regions in mammalian β β β β-globin gene clusters and the control region of bacterial arabinose operons. Although all five methods have quite different theoretical underpinnings, they produce rather similar results on these data sets when their parameters are adjusted to best approximate the experimental data. The optimal parameters for the method based on information content varied little for different regulatory regions of the β β β β-globin gene cluster and hence may be extrapolated to many other regulatory regions. The programs based on maximum allowed mismatches per row have simple parameters whose values can be chosen a priori and thus they may be more useful than the other methods when calibration against known functional sites is not available.

We propose several preprocessing steps to be used before biomarker clustering or classifying for high-throughput Mass Spectrometry (MS) data. These preprocessing steps for the mass spectra are multiple alignment of technical replicates, baseline correction and normalization along the mass/charge axis. While the benefits from baseline correction and alignment seem obvious we studied more carefully the benefit from normalizing using some human prostate cancer SELDI TOF MS data (obtained from the Virginia Prostate Center Tissue and body Fluid Bank and approved by the Eastern Virginia Medical School). We show on these data that our global normalization by scaling helps in distinguishing between different cancer groups as well as between cancer and non-cancer groups. We used the Between to Within sum of squares ratio introduced by Fisher as well as visual inspection to illustrate the improvement brought by the normalization.

Finding certain regularities in a text is an important problem in many areas, for instance in the analysis of biological molecules such as nucleic acids or proteins. In the latter case, the text may be sequences of amino acids or a linear coding of 3D structures, and the regularities then correspond to lexical or structural motifs common to two, or more, proteins. We first recall an earlier algorithm allowing to find these regularities in a flexible way. Then we introduce a generalized version of this algorithm designed for the particular case of protein 3D structures, since these structures present a few peculiarities that make them computationally harder to process. Finally, we give some applications of our new algorithm on concrete examples.

The pyridine nucleotide cycle is a network of salvage and recycling routes maintaining homeostasis of NAD(P) cofactor pool in the cell. Nicotinamide mononucleotide (NMN) deamidase (EC 3.5.1.42), one of the key enzymes of the bacterial pyridine nucleotide cycle, was originally described in Enterobacteria, but the corresponding gene eluded identification for over 30 years. A genomics-based reconstruction of NAD metabolism across hundreds of bacterial species suggested that NMN deamidase reaction is the only possible way of nicotinamide salvage in the marine bacterium Shewanella oneidensis. This prediction was verified via purification of native NMN deamidase from S. oneidensis followed by the identification of the respective gene, termed pncC. Enzymatic characterization of the PncC protein, as well as phenotype analysis of deletion mutants, confirmed its proposed biochemical and physiological function in S. oneidensis. Of the three PncC homologs present in Escherichia coli, NMN deamidase activity was confirmed only for the recombinant purified product of the ygaD gene. A comparative analysis at the level of sequence and three-dimensional structure, which is available for one of the PncC family member, shows no homology with any previously described amidohydrolases. Multiple alignment analysis of functional and nonfunctional PncC homologs, together with NMN docking experiments, allowed us to tentatively identify the active site area and conserved residues therein. An observed broad phylogenomic distribution of predicted functional PncCs in the bacterial kingdom is consistent with a possible role in detoxification of NMN, resulting from NAD utilization by DNA ligase.

Three uncharacterized geminiviruses belonging to the genus Begomovirus were detected in tomato plants in the State of South Baja California (SBC), Mexico, using molecular techniques. General detection was achieved by DNA hybridization with a PHV-A probe. PCR reactions were performed with degenerated primers targeting the coat protein gene and the common or intergenic region. PCR products were cloned, sequenced and compared by local alignment (BLAST) using sequences of reference geminiviruses from the GenBank database (NCBI). Sequences that yielded the highest scores were compared by multiple alignment (MegAlign, DNASTAR). Sequences from three different isolates (LaPS, LaPCh, LaPU3) from the area of La Paz, and one isolate from El Carrizal (CzalB-d21) were thus analyzed. LaPS shared a 93% sequence identity to Tomato severe leaf curl virus (ToSLCV); LaPCh 95% to a partially characterized geminivirus, tentatively named as Tomato mild mottle virus (TMMV); LaPU3 98% to Pepper golden mosaic virus

We determined the nucleotide sequences of blaCARB-4 encoding CARB-4 and deduced a polypeptide of 288 amino acids. The gene was characterized as a variant of group 2c carbenicillin-hydrolyzing beta-lactamases such as PSE-4, PSE-1, and CARB-3. The level of DNA homology between the bla genes for these beta-lactamases varied from 98.7 to 99.9%, while that between these genes and blaCARB-4 encoding CARB-4 was 86.3%. The blaCARB-4 gene was acquired from some other source because it has a G+C content of 39.1%, compared to a G+C content of 67% for typical Pseudomonas aeruginosa genes. DNA sequencing revealed that blaAER-1 shared 60.8% DNA identity with blaPSE-3 encoding PSE-3. The deduced AER-1 beta-lactamase peptide was compared to class A, B, C, and D enzymes and had 57.6% identity with PSE-3, including an STHK tetrad at the active site. For CARB-4 and AER-1, conserved canonical amino acid boxes typical of class A beta-lactamases were identified in a multiple alignment. Analysis of the DN...

Multiple sequence alignments are the usual starting point for analyses of protein structure and evolution. For proteins with repeated, shuffled and missing domains, however, traditional multiple sequence alignment algorithms fail to provide an accurate view of homology between related proteins, because they either assume that the input sequences are globally alignable or require locally alignable regions to appear in the same order in all sequences. In this paper, we present ProDA, a novel system for automated detection and ...

The isocitrate dehydrogenases from the extremely halophilic Archaeon, Huloferux dcnnii, and from the hyperthermophilic Archaeon, Sulfolobus solfaturicus, have been purified to electrophoretic homogeneity. The purified enzymes have been characterised with respect to their cofactor specificities, subunit compositions and their salt and thermal stabilities. N-terminal amino acid sequences have been determined for both enzymes, and multiple alignments with sequences of bacterial and eukaryotic isocitrate dehydrogenases show that the archaeal enzymes most closely resemble the NADP-linked dimeric isocitrate dehydrogenases from the Bacteria.

The braconid wasp subfamily Doryctinae mainly comprises idiobiont ectoparasitoids of other insect larvae. In recent years, however, members of a few genera have been discovered to be associated with galls from various unrelated host plant families, with some of these being gall inducers whereas others are suspected as being predators of gallers. Because of their considerable morphological differences, these gall-associated taxa traditionally have been placed in separate tribes or even in other subfamilies. In this study, we investigate the phylogenetic relationships among representatives of a number of different doryctine genera, including five of its seven gall-associated genera using two genetic markers. Here we analyzed the length-variable 28S sequence data based on secondary structure both excising the unalignable regions and recoding them according to indel length. In addition, multiple alignments were carried out with a range of gap-opening and extension parameters. The combined (28S + CO1) phylogenetic hypotheses obtained, both excluding and recoding the unalignable regions, recover a clade comprising the five gall-associated genera, and most of the analyses using multiple alignments also support this relationship. These results support a scenario in which secondary phytophagy evolves from initially attacking primary gallforming hosts. The relationships recovered are also more congruent with a model that explains the macroevolution of insect plant association in the Doryctinae as reflecting geographic proximity rather than host plant relationships. Further, our phylogenetic hypotheses consistently show that one of the main morphological features employed in the higher level classification of the Doryctinae is actually highly homoplastic.

Correct identification of fish species including their origin requires a compilation of recognized material to verify the conformity of the product with the labelling requirement. Sardine is among the internationally disputed example of species identification conflicts, with the lack of genetic reference material at the Southern part of the Mediterranean. Therefore a method was developed to discriminate between Tunisian small pelagic fish: Sardina pilchardus, Sardinella aurita and Engraulis encrasicolus. DNA extraction from fresh fish and from 12 canned sardine and 2 anchovy-type products, was followed by a PCR method that specifically amplifies a 252 bp fragment of the cytochrome b gene. The new sequences which were deposited in the NCBI GenBank, were searched against a nucleotide sequence database (GenBank) and phylogenetically analyzed with the MEGA software. Multiple alignments of 3 analyzed reference samples belonging to Clupeomorpha species was performed versus the canned samples. Low intraspecific variability was observed for canned anchovy and sardine (<0.05), whereas mean interspecific variability was 0.23. A phylogenetic tree was constructed, and the calculated bootstrap values (BP, 71e100%) were used as indicators of the correct assignment of unknown canned samples to reference species. Postamplification digestion with HaeIII and ALuI restriction enzymes, yielded specific profiles that enabled anchovy to be distinguished from either of the sardine species. This PCR-RFLP was found to be reliable for species identification of canned fish products.

We present MASS (Multiple Alignment by Secondary Structures), a novel highly efficient method for structural alignment of multiple protein molecules and detection of common structural motifs. MASS is based on a two-level alignment, using both secondary structure and atomic representation. Utilizing secondary structure information aids in filtering out noisy solutions and achieves efficiency and robustness. Currently, only a few methods are available for addressing the multiple structural alignment task. In addition to using secondary structure information, the advantage of MASS as compared to these methods is that it is a combination of several important characteristics: (1) While most existing methods are based on series of pairwise comparisons, and thus might miss optimal global solutions, MASS is truly multiple, considering all the molecules simultaneously; (2) MASS is sequence order-independent and thus capable of detecting nontopological structural motifs; (3) MASS is able to detect not only structural motifs, shared by all input molecules, but also motifs shared only by subsets of the molecules. Here, we show the application of MASS to various protein ensembles. We demonstrate its ability to handle a large number (order of tens) of molecules, to detect nontopological motifs and to find biologically meaningful alignments within nonpredefined subsets of the input. In particular, we show how by using conserved structural motifs, one can guide protein-protein docking, which is a notoriously difficult problem. MASS is freely available at http:// bioinfo3d.cs.tau.ac.il/MASS/.

Prediction of protein-RNA interactions at the atomic level of detail is crucial for our ability to understand and interfere with processes such as gene expression and regulation. Here, we investigate protein binding pockets that accommodate extruded nucleotides not involved in RNA base pairing. We observed that most of the protein interacting nucleotides are part of a consecutive fragment of at least two nucleotides, whose rings have significant interactions with the protein. Many of these share the same protein binding cavity and more than 30% of such pairs are π-stacked. Since these local geometries can not be inferred from the nucleotide identities, we present a novel framework for their prediction from the properties of protein binding sites. First, we present a classification of known RNA nucleotide and dinucleotide protein binding sites and identify the common types of shared 3D physico-chemical binding patterns. These are recognized by a new classification methodology which is based on spatial multiple alignment. The shared patterns reveal novel similarities between dinucleotide binding sites of proteins with different overall sequences, folds and functions. Given a protein structure, we use these patterns for the prediction of its RNA dinucleotides binding sites. Based on the binding modes of these nucleotides, we further predict an RNA fragment that interacts with those protein binding sites. With these knowledge-based predictions we construct an RNA fragment that can have a previously unknown sequence and structure. In addition, we provide a drug design application in which the database of all known small molecule binding sites is searched for regions similar to nucleotide and dinucleotide binding patterns, suggesting new fragments and scaffolds that can target them. Keywords protein-RNA interactions; nucleotide and dinucleotide binding sites; physico-chemical binding patterns; multiple binding site alignment; RNA aptamer drug design

The DNA to Protein Translation is performed by detecting open reading frame (ORF) while taking a DNA coding sequence(CDS) as an input. This sequence is then converted into aminoacids taking 3 nucleotides(codons) at a time. Each codon specifies an amino acid. 3 frames for ...

Recently, 454 Life Sciences Corporation proposed a new biochemical approach to DNA sequencing (the 454 sequencing). It is based on the pyrosequencing protocol. The 454 sequencing aims to give reliable output at a low cost and in a short time. The produced sequences are shorter than reads produced by classical methods. Our paper proposes a new DNA assembly algorithm which deals well with such data and outperforms other assembly algorithms used in practice. The constructed SR-ASM algorithm is a heuristic method based on a graph model, the graph being a modified DNA graph proposed for DNA sequencing by hybridization procedure. Other new features of the assembly algorithm are, among others, temporary compression of input sequences, and a new and fast multiple alignment heuristics taking advantage of the way the output data for the 454 sequencing are presented and coded. The usefulness of the algorithm has been proved in tests on raw data generated during sequencing of the whole 1.84 Mbp genome of Prochlorococcus marinus bacteria and also on a part of chromosome 15 of Homo sapiens. The source code of SR-ASM can be downloaded from in the section 'Current research' → 'DNA Assembly'. Among publicly available assemblers our algorithm appeared to generate the best results, especially in the number of produced contigs and in the lengths of the contigs with high similarity to the genome sequence.

We introduce a vector-space embedding of protein sequences which will allow us to find the motifs in a set of proteins. Our method can also be used for the multiple alignment of more than two proteins. It is superior to the existing methods that depend on the order of proteins ...

Structure-based RNA multiple alignment is particularly challenging because covarying mutations make sequence information alone insufficient. Existing tools for RNA multiple alignment first generate pairwise RNA structure alignments and then build the multiple alignment using only sequence information. Here we present PMFastR, an algorithm which iteratively uses a sequence-structure alignment procedure to build a structure-based RNA multiple alignment from one sequence with known structure and a database of sequences from the same family. PMFastR also has low memory consumption allowing for the alignment of large sequences such as 16S and 23S rRNA. The algorithm also provides a method to utilize a multi-core environment. We present results on benchmark data sets from BRAliBase, which shows PMFastR performs comparably to other state-of-the-art programs. Finally, we regenerate 607 Rfam seed alignments and show that our automated process creates multiple alignments similar to the manual...

Motivation: With the increasing availability of large protein–protein interaction networks, the question of protein network alignment is becoming central to systems biology. Network alignment is further delineated into two sub-problems: local alignment, to find small conserved motifs across ...

Hop stunt viroid (HSVd), genus Hostuviroid, family Pospiviroidae is a circular single-stranded RNA 294-303 nt in size, infecting a large number of woody hosts, such as grapevine, Citrus spp. and Prunus spp. In this study, we report the identification and molecular characterization of HSVd variants isolated in Turkey from different naturally infected Prunus sources, including apricot, plum and peach. We determined the nucleotide sequences of eleven isolates and found five new sequence variants of 296 (3 variants) or 297 (2 variants) nt, comparable in length to previously known HSVd isolates. Multiple alignments and phylogenetic analyses showed that one apricot isolate (HSVd.AP1) clustered with the recombinant P-H/cit3 group, whereas all the others (one apricot; HSVd.AP23, two plum; HSVd.PL49 and HSVd.PL278 and one peach, HSVd.PE73) clustered with the Hop group, confirming the molecular variability of HSVd isolates. The sequence variability seems to be more related to the geographical origin of the isolates than to their hosts.

In 2004 and 2005, 51 peach and 5 nectarine trees from different peach growing areas of the East Mediterranean Region of Turkey were analyzed by RT-PCR for the presence of Peach latent mosaic viroid (PLMVd). Most of the samples were from germplasm collections and did not show specific symptoms. PLMVd was detected in three nectarine and eight peach trees. The nucleotide sequence of the eleven PLMVd isolates was determined. Like previously studied PLMVd isolates, Turkish isolates varied in length from 336 to 340 nucleotides. Multiple alignments and phylogenic analyses showed that 31 clones of 11 isolates clustered in PLMVd Group III. Three clones of isolate 99 showed the greatest variability among the isolates characterized in this work and 12 previously characterized isolates. mFold analysis of secondary structures of the three clones of isolate 99 showed that most of the variations are located in a stem involved in the pseudoknot structure, in loop 10 and in the hammerhead arm region. PLMVd isolate 99 showed a high identity with isolate 162.4 from peach cv. Early May Crest.

Savicalin, is a lipocalin found in the hemocytes of the soft tick, Ornithodoros savignyi. It could be assigned to the tick lipocalin family based on BLAST analysis. Savicalin is the first non-salivary gland lipocalin described in ticks. The mature sequence is composed of 188 amino acids with a molecular mass of 21481.9 Da. A homolog for savicalin was found in a whole body EST-library from a related soft tick O. porcinus, while other tick salivary gland derived lipocalins retrieved from the non-redundant sequence database are more distantly related. Homology modeling supports the inclusion of savicalin into the lipocalin family. The model as well as multiple alignments suggests the presence of five disulphide bonds. Two conserved disulphide bonds are found in hard and soft tick lipocalins. A third disulphide bond is shared with the TSGP4-clade of leukotriene C4 binding soft tick lipocalins and a fourth is shared with a lipocalin from the hard tick Ixodes scapularis. The fifth disulphide bond is unique and links  strands D-E. Phylogenetic analysis showed that savicalin is a distant relative of salivary gland derived lipocalins, but groups within a clade that is possibly non-salivary gland derived. It lacks the biogenic amine-binding motif associated with tick histamine and serotonin binding proteins. Expression profiles indicate that savicalin is found in hemocytes, midgut and ovaries, but not in the salivary glands. Up-regulation occurs in hemocytes after bacterial challenge and in midguts and ovaries after feeding. Given its tissue distribution and upregulation of expression, it is possible that this lipocalin functions in tick development after feeding or in an anti-microbial capacity.

We describe a method to identify protein domain boundaries from sequence information alone based on the assumption that hydrophobic residues cluster together in space. SnapDRAGON is a suite of programs developed to predict domain boundaries based on the consistency observed in a set of alternative ab initio three-dimensional (3D) models generated for a given protein multiple sequence alignment. This is achieved by running a distance geometry-based folding technique in conjunction with a 3D-domain assignment algorithm. The overall accuracy of our method in predicting the number of domains for a non-redundant data set of 414 multiple alignments, representing 185 single and 231 multiple-domain proteins, is 72.4 %. Using domain linker regions observed in the tertiary structures associated with each query alignment as the standard of truth, inter-domain boundary positions are delineated with an accuracy of 63.9 % for proteins comprising continuous domains only, and 35.4 % for proteins with discontinuous domains. Overall, domain boundaries are delineated with an accuracy of 51.8 %. The prediction accuracy values are independent of the pair-wise sequence similarities within each of the alignments. These results demonstrate the capability of our method to delineate domains in protein sequences associated with a wide variety of structural domain organisation.

We introduce the online server for PRALINE (http://ibium.cs.vu.nl/programs/pralinewww/), an iterative versatile progressive multiple sequence alignment (MSA) tool. PRALINE provides various MSA optimisation strategies including weighted global and local profile pre-processing, secondary structure-guided alignment and a reliability measure for aligned individual residue positions. The latter can also be used to optimise the alignment when the profile pre-processing strategies are iterated. In addition, we have modelled the server output to enable comprehensive visualisation of the generated alignment and easy figure generation for publications. The alignment is represented in five default colour schemes based on: residue type, position conservation, position reliability, residue hydrophobicity and secondary structure; depending on the options set. We have also implemented a custom colour scheme that allows the user to select which colour will represent one or more amino acids in the alignment. The grouping of sequences, on which the alignment is based, can also be visualised as a dendrogram. The PRALINE algorithm is designed to work more as a toolkit for MSA rather than a one step process.

We propose several preprocessing steps to be used before biomarker clustering or classifying for high-throughput Mass Spectrometry (MS) data. These preprocessing steps for the mass spectra are multiple alignment of technical replicates, baseline correction and normalization along the mass/charge axis. While the benefits from baseline correction and alignment seem obvious we studied more carefully the benefit from normalizing using some human prostate cancer SELDI TOF MS data (obtained from the Virginia Prostate Center Tissue and body Fluid Bank and approved by the Eastern Virginia Medical School). We show on these data that our global normalization by scaling helps in distinguishing between different cancer groups as well as between cancer and non-cancer groups. We used the Between to Within sum of squares ratio introduced by Fisher as well as visual inspection to illustrate the improvement brought by the normalization.

We define and prove properties of the consensus shape for a family of proteins, a protein-like structure that provides a compact summary of the significant structural information for a protein family. If all members of a protein family exhibit a geometric relationship between corresponding alpha carbons then that relationship is preserved in the consensus shape. In particular, distances and angles

Bluetongue is a significant arbovirus infection that has a negative impact on ruminant productivity in Turkey. Twenty-one Turkish BTV isolates were analyzed phylogenetically, based on genome segment 10 (Seg-10) nucleotide sequences. These analyses were used to explore the epidemiological background of individual isolates from both a regional and global perspective. In the regional analysis, the different BTV strains fell into two groups (Group 1 and Group 2). The Turkish virus isolates were localized in Group 1 which contains two subgroups. The neighbor-joining analysis revealed that Seg-10 of majority of the Turkish viruses was closely related to certain other virus strains allocated in the eastern lineage. The Seg-10's of two viruses (TR25 and TR26) were more closely related to strains isolated in the Asia-Australia region. These strains belong to the 'eastern' topotype identified by [Maan, S.

Background Aminopeptidase B (Ap-B; EC 3.4.11.6) catalyzes the cleavage of basic residues at the N-terminus of peptides and processes glucagon into miniglucagon. The enzyme exhibits, in vitro, a residual ability to hydrolyze leukotriene A4 into the pro-inflammatory lipid mediator leukotriene B4. The potential bi-functional nature of Ap-B is supported by close structural relationships with LTA4 hydrolase (LTA4H ; EC 3.3.2.6). A structure-function analysis is necessary for the detailed understanding of the enzymatic mechanisms of Ap-B and to design inhibitors, which could be used to determine the complete in vivo functions of the enzyme. Results The rat Ap-B cDNA was expressed in E. coli and the purified recombinant enzyme was characterized. 18 mutants of the H 325 E XXH X18 E 348 Zn2+-binding motif were constructed and expressed. All mutations were found to abolish the aminopeptidase activity. A multiple alignment of 500 sequences of the M1 family of aminopeptidases was performed to i...

We have built a specialized relational database and a search tool for natural mutants of protein C. It contains 195 entries that include 182 missense and 13 stop mutations. A menu driven search engine allows the user to retrieve stored information for each variant, that include genetic ...

We propose a new alignment procedure that is capable of aligning protein sequences and structures in a unified manner. Recursive dynamic programming (RDP) is a hierarchical method which, on each level of the hierarchy, identifies locally optimal solutions and assembles them into partial alignments of sequences and/or structures. In contrast to classical dynamic programming, RDP can also handle alignment problems that use objective functions not obeying the principle of prefix optimality, e.g. scoring schemes derived from energy potentials of mean force. For such alignment problems, RDP aims at computing solutions that are near-optimal with respect to the involved cost function and biologically meaningful at the same time. Towards this goal, RDP maintains a dynamic balance between different factors governing alignment fitness such as evolutionary relationships and structural preferences. As in the RDP method gaps are not scored explicitly, the problematic assignment of gap cost param...

A group of 4-methoxyphenylacetic acid esters were designed, synthesized and evaluated as potential inhibitors of soybean 15-lipoxygenase (SLO) on the basis of eugenol and esteragol structures. Compounds 7d-e showed the best IC 50 in SLO inhibition (IC 50 = 3.8 and 1.9 lM, respectively). All compounds were docked in SLO active site and showed that carbonyl group of compounds is oriented toward the Fe III-OH moiety in the active site of enzyme and fixed by hydrogen bonding with hydroxyl group. It is assumed that lipophilic interaction of ligand-enzyme would be in charge of inhibiting the enzyme activity. The selectivity of the synthetic esters in inhibiting of 15-HLOb was also compared with 15-HLOa by molecular modeling and multiple alignment techniques.