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PubMed1994

Comparing nucleotide and protein sequences by linguistic methods.

Nucleotide and amino acid sequences can be analyzed and compared by their oligomer compositions. Such methods are fundamentally different from comparison methods based on sequence alignment. They are analogous to the linguistic analysis of human texts. The methods have a wide range of sensitivity and can identify homologous as well as functionally and taxonomically related sequences. Significant sequence dissimilarity can also be identified enabling detection of foreign DNA sequences in genomes, genetic libraries and databases. The simplicity and speed of linguistic methods make them very suitable for database searching and maintenance and as a preliminary step to more specific and time-consuming analysis methods.

Amino Acid Sequence↗

PubMed2003

Identification of a parathyroid hormone in the fish Fugu rubripes.

UNLABELLED: A PTH gene has been isolated from the fish Fugu rubripes. The encoded protein of 80 amino acid has the lowest homology with any of the PTH family members. Fugu PTH(1-34) had 5-fold lower potency than human PTH(1-34) in a mammalian cell system. INTRODUCTION: Parathyroid hormone (PTH) is the major hypercalcemic hormone in higher vertebrates. Fish lack parathyroid glands, but there have numerous attempts to identify and isolate PTH from fish. MATERIALS AND METHODS: Polymerase chain reaction (PCR) was performed with primers based on preliminary data from the Joint Genome Institute database. PCR amplification was performed on genomic DNA isolated from Fugu rubripes. PCR products were purified and DNA was sequenced. All sequence was confirmed from more than one independently amplified PCR product. Multiple sequence alignments were carried out, and the percentage of identities and similarities were calculated. An unrooted phylogenetic tree, using all the known PTH and PTH-related protein (PTHrP) amino acid sequences, was determined. Synthetic peptides were tested in a biological assay that measured cyclic adenosine 3',5'-monophosphate formation in UMR106.1 cells. Rabbit polyclonal antisera specific for N-terminal human PTHrP and one rabbit polyclonal antiserum specific for N terminus hPTH were used to test the cross-reactivity with fPTH(1-34) in immunoblots.

Amino Acid Sequence↗

PubMed2004

BLMT: statistical sequence analysis using N-grams.

UNLABELLED: Statistical analysis of amino acid and nucleotide sequences, especially sequence alignment, is one of the most commonly performed tasks in modern molecular biology. However, for many tasks in bioinformatics, the requirement for the features in an alignment to be consecutive is restrictive and "n-grams" (aka k-tuples) have been used as features instead. N-grams are usually short nucleotide or amino acid sequences of length n, but the unit for a gram may be chosen arbitrarily. The n-gram concept is borrowed from language technologies where n-grams of words form the fundamental units in statistical language models. Despite the demonstrated utility of n-gram statistics for the biology domain, there is currently no publicly accessible generic tool for the efficient calculation of such statistics. Most sequence analysis tools will disregard matches because of the lack of statistical significance in finding short sequences. This article presents the integrated Biological Language Modeling Toolkit (BLMT) that allows efficient calculation of n-gram statistics for arbitrary sequence datasets. AVAILABILITY: BLMT can be downloaded from http://www.cs.cmu.edu/~blmt/source and installed for standalone use on any Unix platform or Unix shell emulation such as Cygwin on the Windows platform. Specific tools and usage details are described in a "readme" file. The n-gram computations carried out by the BLMT are part of a broader set of tools borrowed from language technologies and modified for statistical analysis of biological sequences; these are available at http://flan.blm.cs.cmu.edu/.

Algorithms↗

PubMed1994

[Molecular phylogenies and nucleotide insertion-deletion].

Molecular trees based on the analysis of sequence data can be obtained through parsimony procedures. Such approaches identify evolutionary events (homologies and homoplasies and their location in the tree). Nevertheless, it is not possible generally to analyze directly the information given by the aligned sequences. Noticeably, gaps ("indel") need special coding. Standard procedures for coding gaps offer alternatives which suffer of several weaknesses. In this article a new strategy of coding the sequences is defined in view to express the potential phylogenetic information contained in complex zones with internested insertion/deletion and substitutions, contrary to what is done up to the present. This strategy applies without loss or distortion of information to any case where gaps are present in aligned sequences. According to the hierarchy of internested states of characters (sites), this strategy introduces in the data matrix question marks, "?", which are optimized in fine in the cladogram based on all data. These "?" are not missing data, they are methodological codes, neutral to a priori phylogenetic hypotheses.

Base Sequence↗

PubMed2002

Asymmetric exclusion process and extremal statistics of random sequences.

A mapping is established between sequence alignment, one of the most commonly used tools of computational biology, at a certain choice of scoring parameters and the asymmetric exclusion process, one of the few exactly solvable models of nonequilibrium physics. The statistical significance of sequence alignments is characterized through studying the total hopping current of the discrete time and space version of the asymmetric exclusion process.

Algorithms↗

PubMed1997

Evidence for the assignment of two strains of SPLV to the genus Potyvirus based on coat protein and 3' non-coding region sequence data.

The use of potyvirus-specific primers and subsequent application of the RACE procedure allowed the cloning of the 3' terminal 1088 nucleotides of the genomic RNA of the Taiwan isolate of sweetpotato latent virus (SPLV-T) and the 3' genomic 1085 nucleotides of a SPLV-like virus from China (SPLV-CH). The sequence of an internal part of the presumptive nuclear inclusion b gene was also determined for both isolates. Detailed sequence analyses revealed the presence of consensus motifs which indicated that SPLV-CH and SPLV-T should be regarded as members of the genus Potyvirus. Multiple sequence alignments and phylogenetic analyses were also performed and unambiguously assessed these isolates as strains of a distinct Potyvirus. SPLV was not related to other potyviruses infecting sweetpotato nor to any other sequenced virus. From the presence of the DAG box, SPLV-CH is expected to be a typical aphid transmitted Potyvirus whereas a conceivable explanation is proposed for the non-aphid transmission of SPLV-T.

Amino Acid Sequence↗

PubMed1999

Fine sequence analysis of 60 kb around the Arabidopsis thaliana AtEm1 locus on chromosome III.

The Arabidopsis thaliana Em1 gene has been mapped to the lower arm of chromosome III. Fine analysis of 60 kb around this gene, based largely on identification and sequencing of cognate cDNAs, has allowed us to identify 15 genes or putative genes. Cognate cDNAs exist for ten of these genes, indicating that they are effectively expressed. Analysis by sequence alignment and intracellular localization prediction programs allows attribution of a potential protein product to these genes which show no obvious functional relationship. Comparison of the true exon/intron structure based on cDNA sequences with that proposed by three commonly used prediction programs shows that, in the absence of further information, the results of these predictions on anonymous genomic sequences should be interpreted with caution. Examination of the non-coding sequence showed the presence of a novel repeated, palindromic element. The results of this detailed analysis show that in-depth studies will be necessary to exploit correctly the complete A. thaliana genome sequence.

Arabidopsis↗

PubMed2006

A new D-2-hydroxyacid dehydrogenase with dual coenzyme-specificity from Haloferax mediterranei, sequence analysis and heterologous overexpression.

A gene encoding a new D-2-hydroxyacid dehydrogenase (E.C. 1.1.1.) from the halophilic Archaeon Haloferax mediterranei has been sequenced, cloned and expressed in Escherichia coli cells with the inducible expression plasmid pET3a. The nucleotide sequence analysis showed an open reading frame of 927 bp which encodes a 308 amino acid protein. Multiple amino acid sequence alignments of the D-2-hydroxyacid dehydrogenase from H. mediterranei showed high homology with D-2-hydroxyacid dehydrogenases from different organisms and other enzymes of this family. Analysis of the amino acid sequence showed catalytic residues conserved in hydroxyacid dehydrogenases with d-stereospecificity. In the reductive reaction, the enzyme showed broad substrate specificity, although alpha-ketoisoleucine was the most favourable of all alpha-ketocarboxylic acids tested. Kinetic data revealed that this new D-2-hydroxyacid dehydrogenase from H. mediterranei exhibits dual coenzyme-specificity, using both NADPH and NADH as coenzymes. To date, all D-2-hydroxyacid dehydrogenases have been found to be NADH-dependent. Here, we report the first example of a D-2-hydroxyacid dehydrogenase with dual coenzyme-specificity.

Alcohol Oxidoreductases↗

PubMed2005

Predicting RNA structure using mutual information.

BACKGROUND: With the ever-increasing number of sequenced RNAs and the establishment of new RNA databases, such as the Comparative RNA Web Site and Rfam, there is a growing need for accurately and automatically predicting RNA structures from multiple alignments. Since RNA secondary structure is often conserved in evolution, the well known, but underused, mutual information measure for identifying covarying sites in an alignment can be useful for identifying structural elements. This article presents MIfold, a MATLAB toolbox that employs mutual information, or a related covariation measure, to display and predict conserved RNA secondary structure (including pseudoknots) from an alignment. RESULTS: We show that MIfold can be used to predict simple pseudoknots, and that the performance can be adjusted to make it either more sensitive or more selective. We also demonstrate that the overall performance of MIfold improves with the number of aligned sequences for certain types of RNA sequences. In addition, we show that, for these sequences, MIfold is more sensitive but less selective than the related RNAalifold structure prediction program and is comparable with the COVE structure prediction package. CONCLUSION: MIfold provides a useful supplementary tool to programs such as RNA Structure Logo, RNAalifold and COVE, and should be useful for automatically generating structural predictions for databases such as Rfam.

Algorithms↗

PubMed1992

DNA Translator and Aligner: HyperCard utilities to aid phylogenetic analysis of molecules.

DNA Translator and Aligner are molecular phylogenetics HyperCard stacks for Macintosh computers. They manipulate sequence data to provide graphical gene mapping, conversions, translations and manual multiple-sequence alignment editing. DNA Translator is able to convert documented GenBank or EMBL documented sequences into linearized, rescalable gene maps whose gene sequences are extractable by clicking on the corresponding map button or by selection from a scrolling list. Provided gene maps, complete with extractable sequences, consist of nine metazoan, one yeast, and one ciliate mitochondrial DNAs and three green plant chloroplast DNAs. Single or multiple sequences can be manipulated to aid in phylogenetic analysis. Sequences can be translated between nucleic acids and proteins in either direction with flexible support of alternate genetic codes and ambiguous nucleotide symbols. Multiple aligned sequence output from diverse sources can be converted to Nexus, Hennig86 or PHYLIP format for subsequent phylogenetic analysis. Input or output alignments can be examined with Aligner, a convenient accessory stack included in the DNA Translator package. Aligner is an editor for the manual alignment of up to 100 sequences that toggles between display of matched characters and normal unmatched sequences. DNA Translator also generates graphic displays of amino acid coding and codon usage frequency relative to all other, or only synonymous, codons for approximately 70 select organism-organelle combinations. Codon usage data is compatible with spreadsheet or UWGCG formats for incorporation of additional molecules of interest. The complete package is available via anonymous ftp and is free for non-commercial uses.

Amino Acid Sequence↗

PubMed2006

Computational approaches for predicting the biological effect of p53 missense mutations: a comparison of three sequence analysis based methods.

Prediction of the biological effect of missense substitutions has become important because they are often observed in known or candidate disease susceptibility genes. In this paper, we carried out a 3-step analysis of 1514 missense substitutions in the DNA-binding domain (DBD) of TP53, the most frequently mutated gene in human cancers. First, we calculated two types of conservation scores based on a TP53 multiple sequence alignment (MSA) for each substitution: (i) Grantham Variation (GV), which measures the degree of biochemical variation among amino acids found at a given position in the MSA; (ii) Grantham Deviation (GD), which reflects the 'biochemical distance' of the mutant amino acid from the observed amino acid at a particular position (given by GV). Second, we used a method that combines GV and GD scores, Align-GVGD, to predict the transactivation activity of each missense substitution. We compared our predictions against experimentally measured transactivation activity (yeast assays) to evaluate their accuracy. Finally, the prediction results were compared with those obtained by the program Sorting Intolerant from Tolerant (SIFT) and Dayhoff's classification. Our predictions yielded high prediction accuracy for mutants showing a loss of transactivation ( approximately 88% specificity) with lower prediction accuracy for mutants with transactivation similar to that of the wild-type (67.9 to 71.2% sensitivity). Align-GVGD results were comparable to SIFT (88.3 to 90.6% and 67.4 to 70.3% specificity and sensitivity, respectively) and outperformed Dayhoff's classification (80 and 40.9% specificity and sensitivity, respectively). These results further demonstrate the utility of the Align-GVGD method, which was previously applied to BRCA1. Align-GVGD is available online at http://agvgd.iarc.fr.

Amino Acid Sequence↗

PubMed2006

CorGen--measuring and generating long-range correlations for DNA sequence analysis.

CorGen is a web server that measures long-range correlations in the base composition of DNA and generates random sequences with the same correlation parameters. Long-range correlations are characterized by a power-law decay of the auto correlation function of the GC-content. The widespread presence of such correlations in eukaryotic genomes calls for their incorporation into accurate null models of eukaryotic DNA in computational biology. For example, the score statistics of sequence alignment and the performance of motif finding algorithms are significantly affected by the presence of genomic long-range correlations. We use an expansion-randomization dynamics to efficiently generate the correlated random sequences. The server is available at http://corgen.molgen.mpg.de.

Algorithms↗

PubMed1993

A survey of a functional amino acid of class C beta-lactamase corresponding to Glu166 of class A beta-lactamases.

The class C beta-lactamase of Citrobacter freundii GN346 is a typical cephalosporinase comprising 361 amino acids. The aspartic acid at position 217 and glutamic acid at position 219 in this beta-lactamase were, respectively, previously shown not to be the counterpart of Glu166 (ABL166) in class A beta-lactamases, even though sequence alignment of class A and C enzymes strongly suggested this possibility [(1990) FEBS Lett. 264, 211-214; (1990) J. Bacteriol. 172, 4348-4351]. We tried again to assign candidates for the counterpart of Glu166 through sequence alignment based on other criteria, the glutamic acids at positions 195 and 205 in the class C beta-lactamase being selected. To investigate this possibility, these two glutamic acids were changed to glutamine, lysine or alanine, respectively. All the mutant enzymes showed more than 50% of the activity of the wild-type enzyme, indicating that the possibility was ruled out. These results strongly suggested the possibility that the class C beta-lactamase lacks a functional acidic residue corresponding to Glu166 in class A enzymes.

Alanine↗

PubMed2000

A comparative structural analysis of the ADF/cofilin family.

Actin-depolymerizing factor (ADF) and cofilin define a family of actin-binding proteins essential for the rapid turnover of filamentous actin in vivo. Here we present the 2.0 A crystal structure of Arabidopsis thaliana ADF1 (AtADF1), the first plant crystal structure from the ADF/cofilin (AC) family. Superposition of the four AC isoform structures permits an accurate sequence alignment that differs from previously reported data for the location of vertebrate-specific inserts and reveals a contiguous, vertebrate-specific surface opposite the putative actin-binding surface. Extending the structure-based sequence alignment to include 30 additional isoforms indicates three major groups: vertebrates, plants, and "other eukaryotes." Within these groups, several structurally conserved residues that are not conserved throughout the entire AC family have been identified. Residues that are highly conserved among all isoforms tend to cluster around the tryptophan at position 90 and a structurally conserved kink in alpha-helix 3. Analysis of surface character shows the presence of a hydrophobic patch and a highly conserved acidic cluster, both of which include several residues previously implicated in actin binding.

Actin Depolymerizing Factors↗

PubMed2006

Exploiting sequence and structure homologs to identify protein-protein binding sites.

A rapid increase in the number of experimentally derived three-dimensional structures provides an opportunity to better understand and subsequently predict protein-protein interactions. In this study, structurally conserved residues were derived from multiple structure alignments of the individual components of known complexes and the assigned conservation score was weighted based on the crystallographic B factor to account for the structural flexibility that will result in a poor alignment. Sequence profile and accessible surface area information was then combined with the conservation score to predict protein-protein binding sites using a Support Vector Machine (SVM). The incorporation of the conservation score significantly improved the performance of the SVM. About 52% of the binding sites were precisely predicted (greater than 70% of the residues in the site were identified); 77% of the binding sites were correctly predicted (greater than 50% of the residues in the site were identified), and 21% of the binding sites were partially covered by the predicted residues (some residues were identified). The results support the hypothesis that in many cases protein interfaces require some residues to provide rigidity to minimize the entropic cost upon complex formation.

Adrenodoxin↗

PubMed1993

A novel method of multiple alignment of biopolymer sequences.

A novel algorithm for multiple alignment of biological sequences is suggested. At the first step the DotHelix procedure is employed for construction of motifs, i.e. continuous fragments of local similarity of various "thickness" and strength, and then these motifs are concatenated into chains consistent with the order of letters in the sequences. The algorithm is implemented in the MA-Tools program of the GeneBee package. An example illustrating the effectivity of the algorithm is presented.

Algorithms↗

PubMed2001

The PrP-like protein Doppel gene in sheep and cattle: cDNA sequence and expression.

cDNAs encoding the ovine and bovine prion protein-like protein Doppel (Dpl) have been cloned. Sequencing revealed cDNAs of 2.85 and 3.31 kb from ovine and bovine testicular tissue, in accordance with observations of single transcripts of 3.2 and 3.6 kb on Northern blots. Sequence alignments showed a very high degree of identity between the sheep and cattle Dpl cDNAs, except for a 0.4-kb stretch in the bovine 3' untranslated region and the terminal 3' end of the sequences. The expression pattern of the Dpl gene (Prnd) in adult tissues from both species was compared by Northern blot and RT-PCR analyses. The Prnd gene was expressed strongly in testicular tissue, while low levels of expression were seen in other tissues. The open reading frame of the ovine and bovine sequences encodes a 178-amino acid protein with 95% sequence identity between the two species. Predicted structural features are in close agreement with previous reports for mouse, human, and rat Dpl.

Amino Acid Sequence↗

PubMed2005

Molecular cloning and analysis of a novel teratocyte-specific carboxylesterase from the parasitic wasp, Dinocampus coccinellae.

Teratocytes derived from the embryonic membrane (serosa) of parasitoids are released into the host hemocoel when the parasitoid eggs hatch, where they perform several functions during the post-embryonic stage. A full-length cDNA encoding a putative carboxylesterase was isolated from the teratocytes of Dinocampus coccinellae and was designated as teratocyte-specific carboxylesterase (TSC). It contained an open reading frame of 2571 bp coding for a protein of 857 amino acids with a calculated molecular mass of 89 kDa. The deduced amino acid sequence had many structural features that are highly conserved among serine hydrolases including Ser, Glu and His as a catalytic triad, carboxylesterase type-B (FGGNPNSVTLLGYSAG)/ lipase-serine (VTLLGYSAGA) active sites, and six N-glycosylation sites. Interestingly, the mRNA encoding the TSC gene was expressed exclusively in teratocytes but not in the parasitoid larva or in the non-parasitized host. Most notably, the TSC protein was distinguished by an insertion of 294 amino acids towards the N-terminal region and was flanked by carboxylesterase domains. Furthermore, sequence alignment and homology search revealed these additional amino acids to be unique to TSC and the insertion contributed significantly to its molecular mass resulting in a larger protein than other esterases. In addition to sequence analysis, the possible role of TSC in relation to the host (Coccinella septempunctata) and parasitoid (D. coccinellae) system is discussed.

Amino Acid Sequence↗