119,113 research outputs found
Multiple sequence alignment based on set covers
We introduce a new heuristic for the multiple alignment of a set of
sequences. The heuristic is based on a set cover of the residue alphabet of the
sequences, and also on the determination of a significant set of blocks
comprising subsequences of the sequences to be aligned. These blocks are
obtained with the aid of a new data structure, called a suffix-set tree, which
is constructed from the input sequences with the guidance of the
residue-alphabet set cover and generalizes the well-known suffix tree of the
sequence set. We provide performance results on selected BAliBASE amino-acid
sequences and compare them with those yielded by some prominent approaches
A methodology for determining amino-acid substitution matrices from set covers
We introduce a new methodology for the determination of amino-acid
substitution matrices for use in the alignment of proteins. The new methodology
is based on a pre-existing set cover on the set of residues and on the
undirected graph that describes residue exchangeability given the set cover.
For fixed functional forms indicating how to obtain edge weights from the set
cover and, after that, substitution-matrix elements from weighted distances on
the graph, the resulting substitution matrix can be checked for performance
against some known set of reference alignments and for given gap costs. Finding
the appropriate functional forms and gap costs can then be formulated as an
optimization problem that seeks to maximize the performance of the substitution
matrix on the reference alignment set. We give computational results on the
BAliBASE suite using a genetic algorithm for optimization. Our results indicate
that it is possible to obtain substitution matrices whose performance is either
comparable to or surpasses that of several others, depending on the particular
scenario under consideration
Approximating Edit Distance Within Constant Factor in Truly Sub-Quadratic Time
Edit distance is a measure of similarity of two strings based on the minimum
number of character insertions, deletions, and substitutions required to
transform one string into the other. The edit distance can be computed exactly
using a dynamic programming algorithm that runs in quadratic time. Andoni,
Krauthgamer and Onak (2010) gave a nearly linear time algorithm that
approximates edit distance within approximation factor .
In this paper, we provide an algorithm with running time
that approximates the edit distance within a constant
factor
Family-specific degenerate primer design: a tool to design consensus degenerated oligonucleotides
Designing degenerate PCR primers for templates of unknown nucleotide sequence may be a very difficult task. In this paper, we present a new method to design degenerate primers, implemented in family-specific degenerate primer design (FAS-DPD) computer software, for which the starting point is a multiple alignment of related amino acids or nucleotide sequences. To assess their efficiency, four different genome collections were used, covering a wide range of genomic lengths: Arenavirus ( nucleotides), Baculovirus ( to âbp), Lactobacillus sp. ( to âbp), and Pseudomonas sp. ( to âbp). In each case, FAS-DPD designed primers were tested computationally to measure specificity. Designed primers for Arenavirus and Baculovirus were tested experimentally. The method presented here is useful for designing degenerate primers on collections of related protein sequences, allowing detection of new family members.Fil: Iserte, Javier Alonso. Universidad Nacional de Quilmes. Departamento de Ciencia y TecnologĂa. Laboratorio de IngenierĂa GenĂ©tica y BiologĂa Molecular y Celular. Ărea de Virosis Emergentes y ZoonĂłtica; Argentina. Consejo Nacional de Investigaciones CientĂficas y TĂ©cnicas; ArgentinaFil: Stephan, Betina InĂ©s. Universidad Nacional de Quilmes. Departamento de Ciencia y TecnologĂa. Laboratorio de IngenierĂa GenĂ©tica y BiologĂa Molecular y Celular. Ărea de Virosis Emergentes y ZoonĂłtica; Argentina. Consejo Nacional de Investigaciones CientĂficas y TĂ©cnicas; ArgentinaFil: Goñi, Sandra Elizabeth. Universidad Nacional de Quilmes. Departamento de Ciencia y TecnologĂa. Laboratorio de IngenierĂa GenĂ©tica y BiologĂa Molecular y Celular. Ărea de Virosis Emergentes y ZoonĂłtica; Argentina. Consejo Nacional de Investigaciones CientĂficas y TĂ©cnicas; ArgentinaFil: Borio, Cristina Silvia. Universidad Nacional de Quilmes. Departamento de Ciencia y TecnologĂa. Laboratorio de IngenierĂa GenĂ©tica y BiologĂa Molecular y Celular. Ărea de Virosis Emergentes y ZoonĂłtica; Argentina. Consejo Nacional de Investigaciones CientĂficas y TĂ©cnicas; ArgentinaFil: Ghiringhelli, Pablo Daniel. Universidad Nacional de Quilmes. Departamento de Ciencia y TecnologĂa. Laboratorio de IngenierĂa GenĂ©tica y BiologĂa Molecular y Celular. Ărea Virus de Insectos; Argentina. Consejo Nacional de Investigaciones CientĂficas y TĂ©cnicas; ArgentinaFil: Lozano, Mario Enrique. Consejo Nacional de Investigaciones CientĂficas y TĂ©cnicas; Argentina. Universidad Nacional de Quilmes. Departamento de Ciencia y TecnologĂa. Laboratorio de IngenierĂa GenĂ©tica y BiologĂa Molecular y Celular. Ărea de Virosis Emergentes y ZoonĂłtica; Argentin
Improved annotation of 3' untranslated regions and complex loci by combination of strand-specific direct RNA sequencing, RNA-seq and ESTs
The reference annotations made for a genome sequence provide the framework
for all subsequent analyses of the genome. Correct annotation is particularly
important when interpreting the results of RNA-seq experiments where short
sequence reads are mapped against the genome and assigned to genes according to
the annotation. Inconsistencies in annotations between the reference and the
experimental system can lead to incorrect interpretation of the effect on RNA
expression of an experimental treatment or mutation in the system under study.
Until recently, the genome-wide annotation of 3-prime untranslated regions
received less attention than coding regions and the delineation of intron/exon
boundaries. In this paper, data produced for samples in Human, Chicken and A.
thaliana by the novel single-molecule, strand-specific, Direct RNA Sequencing
technology from Helicos Biosciences which locates 3-prime polyadenylation sites
to within +/- 2 nt, were combined with archival EST and RNA-Seq data. Nine
examples are illustrated where this combination of data allowed: (1) gene and
3-prime UTR re-annotation (including extension of one 3-prime UTR by 5.9 kb);
(2) disentangling of gene expression in complex regions; (3) clearer
interpretation of small RNA expression and (4) identification of novel genes.
While the specific examples displayed here may become obsolete as genome
sequences and their annotations are refined, the principles laid out in this
paper will be of general use both to those annotating genomes and those seeking
to interpret existing publically available annotations in the context of their
own experimental dataComment: 44 pages, 9 figure
Who Watches the Watchmen? An Appraisal of Benchmarks for Multiple Sequence Alignment
Multiple sequence alignment (MSA) is a fundamental and ubiquitous technique
in bioinformatics used to infer related residues among biological sequences.
Thus alignment accuracy is crucial to a vast range of analyses, often in ways
difficult to assess in those analyses. To compare the performance of different
aligners and help detect systematic errors in alignments, a number of
benchmarking strategies have been pursued. Here we present an overview of the
main strategies--based on simulation, consistency, protein structure, and
phylogeny--and discuss their different advantages and associated risks. We
outline a set of desirable characteristics for effective benchmarking, and
evaluate each strategy in light of them. We conclude that there is currently no
universally applicable means of benchmarking MSA, and that developers and users
of alignment tools should base their choice of benchmark depending on the
context of application--with a keen awareness of the assumptions underlying
each benchmarking strategy.Comment: Revie
Towards trajectory anonymization: a generalization-based approach
Trajectory datasets are becoming popular due to the massive usage of GPS and locationbased services. In this paper, we address privacy issues regarding the identification of individuals in static trajectory datasets. We first adopt the notion of k-anonymity to trajectories and propose a novel generalization-based approach for anonymization of trajectories. We further show that releasing
anonymized trajectories may still have some privacy leaks. Therefore we propose a randomization based reconstruction algorithm for releasing anonymized trajectory data and also present how the underlying techniques can be adapted to other anonymity standards. The experimental results on real and synthetic trajectory datasets show the effectiveness of the proposed techniques
MRFalign: Protein Homology Detection through Alignment of Markov Random Fields
Sequence-based protein homology detection has been extensively studied and so
far the most sensitive method is based upon comparison of protein sequence
profiles, which are derived from multiple sequence alignment (MSA) of sequence
homologs in a protein family. A sequence profile is usually represented as a
position-specific scoring matrix (PSSM) or an HMM (Hidden Markov Model) and
accordingly PSSM-PSSM or HMM-HMM comparison is used for homolog detection. This
paper presents a new homology detection method MRFalign, consisting of three
key components: 1) a Markov Random Fields (MRF) representation of a protein
family; 2) a scoring function measuring similarity of two MRFs; and 3) an
efficient ADMM (Alternating Direction Method of Multipliers) algorithm aligning
two MRFs. Compared to HMM that can only model very short-range residue
correlation, MRFs can model long-range residue interaction pattern and thus,
encode information for the global 3D structure of a protein family.
Consequently, MRF-MRF comparison for remote homology detection shall be much
more sensitive than HMM-HMM or PSSM-PSSM comparison. Experiments confirm that
MRFalign outperforms several popular HMM or PSSM-based methods in terms of both
alignment accuracy and remote homology detection and that MRFalign works
particularly well for mainly beta proteins. For example, tested on the
benchmark SCOP40 (8353 proteins) for homology detection, PSSM-PSSM and HMM-HMM
succeed on 48% and 52% of proteins, respectively, at superfamily level, and on
15% and 27% of proteins, respectively, at fold level. In contrast, MRFalign
succeeds on 57.3% and 42.5% of proteins at superfamily and fold level,
respectively. This study implies that long-range residue interaction patterns
are very helpful for sequence-based homology detection. The software is
available for download at http://raptorx.uchicago.edu/download/.Comment: Accepted by both RECOMB 2014 and PLOS Computational Biolog
- âŠ