Brief. Bioinformatics - Benchmarking of viral haplotype reconstruction programmes: an overview of the capacities and limitations of currently available programmes.

Tópicos

{ sequenc(1873) structur(1644) protein(1328) }
{ learn(2355) train(1041) set(1003) }
{ method(984) reconstruct(947) comput(926) }
{ data(3008) multipl(1320) sourc(1022) }
{ data(2317) use(1299) case(1017) }
{ clinic(1479) use(1117) guidelin(835) }
{ howev(809) still(633) remain(590) }
{ activ(1138) subject(705) human(624) }
{ implement(1333) system(1263) develop(1122) }
{ model(3404) distribut(989) bayesian(671) }
{ can(774) often(719) complex(702) }
{ error(1145) method(1030) estim(1020) }
{ general(901) number(790) one(736) }
{ model(2656) set(1616) predict(1553) }
{ age(1611) year(1155) adult(843) }
{ signal(2180) analysi(812) frequenc(800) }
{ first(2504) two(1366) second(1323) }
{ patient(2315) diseas(1263) diabet(1191) }
{ take(945) account(800) differ(722) }
{ studi(2440) review(1878) systemat(933) }
{ concept(1167) ontolog(924) domain(897) }
{ control(1307) perform(991) simul(935) }
{ perform(999) metric(946) measur(919) }
{ compound(1573) activ(1297) structur(1058) }
{ monitor(1329) mobil(1314) devic(1160) }
{ group(2977) signific(1463) compar(1072) }
{ gene(2352) biolog(1181) express(1162) }
{ time(1939) patient(1703) rate(768) }
{ patient(1821) servic(1111) care(1106) }
{ use(1733) differ(960) four(931) }
{ drug(1928) target(777) effect(648) }
{ survey(1388) particip(1329) question(1065) }
{ estim(2440) model(1874) function(577) }
{ activ(1452) weight(1219) physic(1104) }
{ method(1969) cluster(1462) data(1082) }
{ imag(1947) propos(1133) code(1026) }
{ data(1737) use(1416) pattern(1282) }
{ inform(2794) health(2639) internet(1427) }
{ system(1976) rule(880) can(841) }
{ measur(2081) correl(1212) valu(896) }
{ imag(1057) registr(996) error(939) }
{ bind(1733) structur(1185) ligand(1036) }
{ method(1219) similar(1157) match(930) }
{ featur(3375) classif(2383) classifi(1994) }
{ imag(2830) propos(1344) filter(1198) }
{ network(2748) neural(1063) input(814) }
{ imag(2675) segment(2577) method(1081) }
{ motion(1329) object(1292) video(1091) }
{ assess(1506) score(1403) qualiti(1306) }
{ treatment(1704) effect(941) patient(846) }
{ surgeri(1148) surgic(1085) robot(1054) }
{ framework(1458) process(801) describ(734) }
{ problem(2511) optim(1539) algorithm(950) }
{ chang(1828) time(1643) increas(1301) }
{ algorithm(1844) comput(1787) effici(935) }
{ extract(1171) text(1153) clinic(932) }
{ method(1557) propos(1049) approach(1037) }
{ data(1714) softwar(1251) tool(1186) }
{ design(1359) user(1324) use(1319) }
{ model(2220) cell(1177) simul(1124) }
{ care(1570) inform(1187) nurs(1089) }
{ search(2224) databas(1162) retriev(909) }
{ featur(1941) imag(1645) propos(1176) }
{ case(1353) use(1143) diagnosi(1136) }
{ data(3963) clinic(1234) research(1004) }
{ studi(1410) differ(1259) use(1210) }
{ risk(3053) factor(974) diseas(938) }
{ research(1085) discuss(1038) issu(1018) }
{ system(1050) medic(1026) inform(1018) }
{ import(1318) role(1303) understand(862) }
{ model(2341) predict(2261) use(1141) }
{ visual(1396) interact(850) tool(830) }
{ perform(1367) use(1326) method(1137) }
{ studi(1119) effect(1106) posit(819) }
{ blood(1257) pressur(1144) flow(957) }
{ spatial(1525) area(1432) region(1030) }
{ record(1888) medic(1808) patient(1693) }
{ health(3367) inform(1360) care(1135) }
{ model(3480) simul(1196) paramet(876) }
{ ehr(2073) health(1662) electron(1139) }
{ state(1844) use(1261) util(961) }
{ research(1218) medic(880) student(794) }
{ patient(2837) hospit(1953) medic(668) }
{ medic(1828) order(1363) alert(1069) }
{ cost(1906) reduc(1198) effect(832) }
{ sampl(1606) size(1419) use(1276) }
{ intervent(3218) particip(2042) group(1664) }
{ use(2086) technolog(871) perceiv(783) }
{ can(981) present(881) function(850) }
{ analysi(2126) use(1163) compon(1037) }
{ health(1844) social(1437) communiti(874) }
{ structur(1116) can(940) graph(676) }
{ high(1669) rate(1365) level(1280) }
{ cancer(2502) breast(956) screen(824) }
{ use(976) code(926) identifi(902) }
{ result(1111) use(1088) new(759) }
{ decis(3086) make(1611) patient(1517) }
{ process(1125) use(805) approach(778) }
{ method(2212) result(1239) propos(1039) }
{ detect(2391) sensit(1101) algorithm(908) }

Resumo

Viral haplotype reconstruction from a set of observed reads is one of the most challenging problems in bioinformatics today. Next-generation sequencing technologies enable us to detect single-nucleotide polymorphisms (SNPs) of haplotypes-even if the haplotypes appear at low frequencies. However, there are two major problems. First, we need to distinguish real SNPs from sequencing errors. Second, we need to determine which SNPs occur on the same haplotype, which cannot be inferred from the reads if the distance between SNPs on a haplotype exceeds the read length. We conducted an independent benchmarking study that directly compares the currently available viral haplotype reconstruction programmes. We also present nine in silico data sets that we generated to reflect biologically plausible populations. For these data sets, we simulated 454 and Illumina reads and applied the programmes to test their capacity to reconstruct whole genomes and individual genes. We developed a novel statistical framework to demonstrate the strengths and limitations of the programmes. Our benchmarking demonstrated that all the programmes we tested performed poorly when sequence divergence was low and failed to recover haplotype populations with rare haplotypes.

Resumo Limpo

viral haplotyp reconstruct set observ read one challeng problem bioinformat today nextgener sequenc technolog enabl us detect singlenucleotid polymorph snps haplotypeseven haplotyp appear low frequenc howev two major problem first need distinguish real snps sequenc error second need determin snps occur haplotyp infer read distanc snps haplotyp exceed read length conduct independ benchmark studi direct compar current avail viral haplotyp reconstruct programm also present nine silico data set generat reflect biolog plausibl popul data set simul illumina read appli programm test capac reconstruct whole genom individu gene develop novel statist framework demonstr strength limit programm benchmark demonstr programm test perform poor sequenc diverg low fail recov haplotyp popul rare haplotyp

Resumos Similares

J Chem Inf Model - Improved helix and kink characterization in membrane proteins allows evaluation of kink sequence predictors. ( 0,712898027230285 )
IEEE Trans Pattern Anal Mach Intell - Unsupervised Adaptation Across Domain Shifts By Generating Intermediate Data Representations. ( 0,706975814181763 )
Brief. Bioinformatics - Alpha shape and Delaunay triangulation in studies of protein-related interactions. ( 0,702719415049059 )
Med Biol Eng Comput - The influence of alignment-free sequence representations on the semi-supervised classification of class C G protein-coupled receptors: semi-supervised classification of class C GPCRs. ( 0,702473657242732 )
Comput Biol Chem - Support vector machine with a Pearson VII function kernel for discriminating halophilic and non-halophilic proteins. ( 0,701536050191488 )
J Chem Inf Model - Protein secondary structure prediction with SPARROW. ( 0,700747067349869 )
Comput Methods Programs Biomed - Discriminating protein structure classes by incorporating Pseudo Average Chemical Shift to Chou's general PseAAC and Support Vector Machine. ( 0,693352864333698 )
J. Comput. Biol. - The irredundant class method for remote homology detection of protein sequences. ( 0,688005670007217 )
J. Comput. Biol. - Combinatorics of -structures. ( 0,679510863343728 )
J. Comput. Biol. - Simultaneous alignment and folding of protein sequences. ( 0,660758747155447 )
Comput. Biol. Med. - miRClassify: an advanced web server for miRNA family classification and annotation. ( 0,655394301385062 )
Brief. Bioinformatics - Taxonomic binning of metagenome samples generated by next-generation sequencing technologies. ( 0,651956744257374 )
Comput Biol Chem - Bacterial protein structures reveal phylum dependent divergence. ( 0,651217144763179 )
Sci Data - A draft genome for the African crocodilian trypanosome Trypanosoma grayi. ( 0,650582120580198 )
J. Comput. Biol. - Evaluating, comparing, and interpreting protein domain hierarchies. ( 0,65015258909947 )
Comput Biol Chem - A novel feature representation method based on Chou's pseudo amino acid composition for protein structural class prediction. ( 0,645919532050871 )
J Chem Inf Model - Structural effects of pH and deacylation on surfactant protein C in an organic solvent mixture: a constant-pH MD study. ( 0,645208963831595 )
J. Comput. Biol. - Nonparametric combinatorial sequence models. ( 0,644290958193806 )
J. Comput. Biol. - SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. ( 0,643875325506181 )
Comput Biol Chem - The frequency of poly(G) tracts in the human genome and their use as a sensor of DNA damage. ( 0,641063527169078 )
Sci Data - Long-read, whole-genome shotgun sequence data for five model organisms. ( 0,636962425340551 )
Brief. Bioinformatics - Comparative genomics approach to detecting split-coding regions in a low-coverage genome: lessons from the chimaera Callorhinchus milii (Holocephali, Chondrichthyes). ( 0,636668808808428 )
J Chem Inf Model - Tertiary structure prediction of RNA-RNA complexes using a secondary structure and fragment-based method. ( 0,63661305999562 )
Comput Biol Chem - Statistical analysis and exposure status classification of transmembrane beta barrel residues. ( 0,633182405684755 )
J. Comput. Biol. - Statistical significance of threading scores. ( 0,632693586341872 )
Comput Biol Chem - Multi-nucleation and vectorial folding pathways of large helix protein. ( 0,632566844787898 )
Comput Biol Chem - Protein fold recognition based on functional domain composition. ( 0,630875939469852 )
Comput Biol Chem - ProSTRIP: A method to find similar structural repeats in three-dimensional protein structures. ( 0,629477791209819 )
Comput. Biol. Med. - An insight into the molecular basis for convergent evolution in fish antifreeze Proteins. ( 0,629120642302878 )
Curr Protoc Bioinformatics - Using the RNAstructure Software Package to Predict Conserved RNA Structures. ( 0,62873550091256 )
Brief. Bioinformatics - De novo assembly of short sequence reads. ( 0,627120897687471 )
J. Comput. Biol. - Determining a singleton attractor of a boolean network with nested canalyzing functions. ( 0,626016920153065 )
Brief. Bioinformatics - Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. ( 0,623857038363282 )
Comput Biol Chem - Analysis of sequence repeats of proteins in the PDB. ( 0,621431407526629 )
Comput Biol Chem - A novel empirical mutual information approach to identify co-evolving amino acid positions of influenza A viruses. ( 0,619725459215876 )
Brief. Bioinformatics - New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing. ( 0,61776337145003 )
Brief. Bioinformatics - Systematic identification of Class I HDAC substrates. ( 0,617004820496012 )
J. Comput. Biol. - IDBA-MTP: A Hybrid Metatranscriptomic Assembler Based on Protein Information. ( 0,615407339476177 )
BMC Med Inform Decis Mak - Efficient protein structure search using indexing methods. ( 0,615179656529241 )
J Chem Inf Model - Modules identification in protein structures: the topological and geometrical solutions. ( 0,614176067497419 )
Comput. Biol. Med. - Application of 2D graphic representation of protein sequence based on Huffman tree method. ( 0,613737052823838 )
Comput. Biol. Med. - Improving protein secondary structure prediction using a multi-modal BP method. ( 0,613483817813372 )
J. Comput. Biol. - eALPS: estimating abundance levels in pooled sequencing using available genotyping data. ( 0,610618178523853 )
J Chem Inf Model - Kink characterization and modeling in transmembrane protein structures. ( 0,608957790827624 )
Comput Math Methods Med - DV-curve representation of protein sequences and its application. ( 0,607351923717091 )
Comput Biol Chem - ProCoCoA: A quantitative approach for analyzing protein core composition. ( 0,606845578073571 )
J Integr Bioinform - Predicting protein distance maps according to physicochemical properties. ( 0,60662390962653 )
Comput Biol Chem - Characterizing regions in the human genome unmappable by next-generation-sequencing at the read length of 1000 bases. ( 0,606071366137855 )
J Biomed Inform - A kinetic model-based algorithm to classify NGS short reads by their allele origin. ( 0,604965978972308 )
J Chem Inf Model - Building a knowledge-based statistical potential by capturing high-order inter-residue interactions and its applications in protein secondary structure assessment. ( 0,603585950052379 )
J Chem Inf Model - ProBiS-database: precalculated binding site similarities and local pairwise alignments of PDB structures. ( 0,603280673280566 )
Comput Biol Chem - Identical sequence patterns in the ends of exons and introns of human protein-coding genes. ( 0,603142966638662 )
Comput Biol Chem - Computational insight into nitration of human myoglobin. ( 0,603056275314408 )
Brief. Bioinformatics - A survey of tools for variant analysis of next-generation genome sequencing data. ( 0,600515750714636 )
J Integr Bioinform - A hierarchical approach to protein fold prediction. ( 0,600291734138952 )
Comput. Biol. Med. - A content and structural assessment of oxidative motifs across a diverse set of life forms. ( 0,599424864292064 )
Brief. Bioinformatics - Ortholog identification in the presence of domain architecture rearrangement. ( 0,598408622190215 )
Med Biol Eng Comput - Enhanced spatio-temporal alignment of plantar pressure image sequences using B-splines. ( 0,598011102269106 )
Brief. Bioinformatics - Automated glycopeptide analysis--review of current state and future directions. ( 0,598008474478757 )
J. Comput. Biol. - Mapping reads on a genomic sequence: an algorithmic overview and a practical comparative analysis. ( 0,595614384572892 )
Comput Biol Chem - Identification and characterization of lysine-methylated sites on histones and non-histone proteins. ( 0,591979165062061 )
Comput. Biol. Med. - The possible role of HSPs on Beh?et's disease: a bioinformatic approach. ( 0,591309703916503 )
Comput Biol Chem - Computational determination of the orientation of a heat repeat-like domain of DNA-PKcs. ( 0,591103817526856 )
Comput Math Methods Med - Uses of phage display in agriculture: sequence analysis and comparative modeling of late embryogenesis abundant client proteins suggest protein-nucleic acid binding functionality. ( 0,590308897701014 )
J. Comput. Biol. - AREM: aligning short reads from ChIP-sequencing by expectation maximization. ( 0,590073665219762 )
Sci Data - Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus. ( 0,589115402111166 )
Comput Biol Chem - Human-chimpanzee alignment: ortholog exponentials and paralog power laws. ( 0,586423323110777 )
Brief. Bioinformatics - Analysis of insertion-deletion from deep-sequencing data: software evaluation for optimal detection. ( 0,586320996387115 )
J. Comput. Biol. - Reconstructing the history of large-scale genomic changes: biological questions and computational challenges. ( 0,586296699465118 )
IEEE Trans Pattern Anal Mach Intell - Conditional Alignment Random Fields for Multiple Motion Sequence Alignment. ( 0,584959099300832 )
Comput Biol Chem - The challenge of annotating protein sequences: The tale of eight domains of unknown function in Pfam. ( 0,584626579695252 )
Brief. Bioinformatics - Ultrafast clustering algorithms for metagenomic sequence analysis. ( 0,583987748051381 )
Comput Biol Chem - Identification of putative and potential cross-reactive chickpea (Cicer arietinum) allergens through an in silico approach. ( 0,583021363838885 )
J Integr Bioinform - Exceptional single strand DNA word symmetry: analysis of evolutionary potentialities. ( 0,581610440869604 )
Comput Math Methods Med - Quad-PRE: a hybrid method to predict protein quaternary structure attributes. ( 0,581151981254362 )
Comput Methods Programs Biomed - Pinda: a web service for detection and analysis of intraspecies gene duplication events. ( 0,581141138888986 )
IEEE Trans Pattern Anal Mach Intell - Learning spectral descriptors for deformable shape correspondence. ( 0,58107835906504 )
J Chem Inf Model - Parallel and antiparallel ?-strands differ in amino acid composition and availability of short constituent sequences. ( 0,579181983636325 )
Brief. Bioinformatics - Computational challenges of sequence classification in microbiomic data. ( 0,579031938272636 )
J Chem Inf Model - Predicting order and disorder for ?-peptide foldamers in water. ( 0,578754852261287 )
Comput Methods Programs Biomed - Protein secondary structure prediction using modular reciprocal bidirectional recurrent neural networks. ( 0,576598583968076 )
Comput. Biol. Med. - Cutaneous amyloidoses: a minimum common denominator in their amino acid sequence. ( 0,575158573746869 )
Brief. Bioinformatics - A practical guide for the computational selection of residues to be experimentally characterized in protein families. ( 0,575145351075016 )
J Biomed Inform - A similarity network approach for the analysis and comparison of protein sequence/structure sets. ( 0,575067394659449 )
J Chem Inf Model - Data-driven high-throughput prediction of the 3-D structure of small molecules: review and progress. ( 0,575038786476228 )
Comput. Biol. Med. - A context evaluation approach for structural comparison of proteins using cross entropy over n-gram modelling. ( 0,573087134056008 )
J Chem Inf Model - String kernels and high-quality data set for improved prediction of kinked helices in a-helical membrane proteins. ( 0,572613179937423 )
Brief. Bioinformatics - Functional assignment of metagenomic data: challenges and applications. ( 0,572283859441439 )
J. Comput. Biol. - Accurate estimations of evolutionary times in the context of strong CpG hypermutability. ( 0,571358642255702 )
Brief. Bioinformatics - Base-calling for next-generation sequencing platforms. ( 0,571336369607927 )
J Chem Inf Model - Comparative analysis of threshold and tessellation methods for determining protein contacts. ( 0,568957268201921 )
Sci Data - Comprehensive analysis of the venom gland transcriptome of the spider Dolomedes fimbriatus. ( 0,568770015322507 )
J Chem Inf Model - Protein secondary structure classification revisited: processing DSSP information with PSSC. ( 0,567291559573739 )
J. Comput. Biol. - Efficient traversal of beta-sheet protein folding pathways using ensemble models. ( 0,565853815671451 )
J. Comput. Biol. - The generating function approach for Peptide identification in spectral networks. ( 0,564809247362662 )
J Chem Inf Model - Protein structural statistics with PSS. ( 0,564573252520442 )
J. Comput. Biol. - Optimization of profile-to-profile alignment parameters for one-dimensional threading. ( 0,56418667589691 )
J. Comput. Biol. - Statistical significance of optical map alignments. ( 0,564157498878174 )
J. Comput. Biol. - Computing the probability of RNA hairpin and multiloop formation. ( 0,563088093436329 )
J. Comput. Biol. - ComB: SNP calling and mapping analysis for color and nucleotide space platforms. ( 0,562628084375937 )