Comput. Biol. Med. - Intron identification approaches based on weighted features and fuzzy decision trees.

Tópicos

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

Resumo

Current computational predictions of splice sites largely depend on the sequence patterns of known intronic sequence features (ISFs) described in the classical intron definition model (IDM). The computation-oriented IDM (CO-IDM) clearly provides more specific and concrete information for describing intron flanks of splice sites (IFSSs). In the paper, we proposed a novel approach of fuzzy decision trees (FDTs) which utilize (1) weighted ISFs of twelve uni-frame patterns (UFPs) and forty-five multi-frame patterns (MFPs) and (2) gain ratios to improve the performances in identifying an intron. First, we fuzzified extracted features from genomic sequences using membership functions with an unsupervised self-organizing map (SOM) technique. Then, we brought in different viewpoints of globally weighting and crossly referring in generating fuzzy rules, which are interpretable and useful for biologists to verify whether a sequence is an intron or not. Finally, the experimental results revealed the effectiveness of the proposed method in improving the identification accuracy. Besides, we also implemented an on-line intronic identifier to infer an unknown genomic sequence.

Resumo Limpo

current comput predict splice site larg depend sequenc pattern known intron sequenc featur isf describ classic intron definit model idm computationori idm coidm clear provid specif concret inform describ intron flank splice site ifsss paper propos novel approach fuzzi decis tree fdts util weight isf twelv unifram pattern ufp fortyf multifram pattern mfps gain ratio improv perform identifi intron first fuzzifi extract featur genom sequenc use membership function unsupervis selforgan map som techniqu brought differ viewpoint global weight crossli refer generat fuzzi rule interpret use biologist verifi whether sequenc intron final experiment result reveal effect propos method improv identif accuraci besid also implement onlin intron identifi infer unknown genom sequenc

Resumos Similares

Comput Math Methods Med - Quad-PRE: a hybrid method to predict protein quaternary structure attributes. ( 0,85917037410478 )
J Chem Inf Model - Modules identification in protein structures: the topological and geometrical solutions. ( 0,807115300689893 )
Comput. Biol. Med. - Improving protein secondary structure prediction using a multi-modal BP method. ( 0,805285148212856 )
Comput. Biol. Med. - A context evaluation approach for structural comparison of proteins using cross entropy over n-gram modelling. ( 0,798484785886634 )
BMC Med Inform Decis Mak - Efficient protein structure search using indexing methods. ( 0,796255042095651 )
Comput Biol Chem - Bacterial protein structures reveal phylum dependent divergence. ( 0,793590704201961 )
Comput Biol Chem - Human-chimpanzee alignment: ortholog exponentials and paralog power laws. ( 0,79107318556832 )
Comput Biol Chem - Identification and characterization of lysine-methylated sites on histones and non-histone proteins. ( 0,790596066570597 )
Comput. Biol. Med. - Signal peptide discrimination and cleavage site identification using SVM and NN. ( 0,787074051449627 )
Comput Biol Chem - Inferring biological basis about psychrophilicity by interpreting the rules generated from the correctly classified input instances by a classifier. ( 0,783028195822836 )
Comput Biol Chem - Statistical analysis and exposure status classification of transmembrane beta barrel residues. ( 0,77874899286431 )
J Integr Bioinform - A hierarchical approach to protein fold prediction. ( 0,777658880394425 )
Comput Biol Chem - Analysis of sequence repeats of proteins in the PDB. ( 0,77596116228229 )
Comput Biol Chem - Protein fold recognition based on functional domain composition. ( 0,775333822944997 )
Comput Biol Chem - Characterizing regions in the human genome unmappable by next-generation-sequencing at the read length of 1000 bases. ( 0,770905450137561 )
J Chem Inf Model - ProBiS-database: precalculated binding site similarities and local pairwise alignments of PDB structures. ( 0,770889444946954 )
J. Comput. Biol. - A novel technique for detecting putative horizontal gene transfer in the sequence space. ( 0,7689570974555 )
J. Comput. Biol. - Evaluating, comparing, and interpreting protein domain hierarchies. ( 0,768457164607815 )
Brief. Bioinformatics - De novo assembly of short sequence reads. ( 0,767136432185581 )
Comput Math Methods Med - Na?ve Bayes classifier with feature selection to identify phage virion proteins. ( 0,766879743942514 )
Comput. Biol. Med. - An insight into the molecular basis for convergent evolution in fish antifreeze Proteins. ( 0,766773958387981 )
J Chem Inf Model - Context-based features enhance protein secondary structure prediction accuracy. ( 0,766481570457896 )
Comput Biol Chem - ProSTRIP: A method to find similar structural repeats in three-dimensional protein structures. ( 0,766453381267259 )
J. Comput. Biol. - IDBA-MTP: A Hybrid Metatranscriptomic Assembler Based on Protein Information. ( 0,759967265058862 )
Comput Biol Chem - ProCoCoA: A quantitative approach for analyzing protein core composition. ( 0,756707920332993 )
Comput. Biol. Med. - Predicting protein-binding RNA nucleotides using the feature-based removal of data redundancy and the interaction propensity of nucleotide triplets. ( 0,756505377733851 )
Brief. Bioinformatics - Systematic identification of Class I HDAC substrates. ( 0,756006118169433 )
J Chem Inf Model - Dihedral-based segment identification and classification of biopolymers II: polynucleotides. ( 0,751224190750912 )
Comput Biol Chem - Computational insight into nitration of human myoglobin. ( 0,749738112961616 )
Comput Biol Chem - The frequency of poly(G) tracts in the human genome and their use as a sensor of DNA damage. ( 0,749575391719773 )
Brief. Bioinformatics - New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing. ( 0,74633281020835 )
J Chem Inf Model - Protein secondary structure prediction with SPARROW. ( 0,746300825772205 )
J Chem Inf Model - Tertiary structure prediction of RNA-RNA complexes using a secondary structure and fragment-based method. ( 0,746020037352004 )
J. Comput. Biol. - Simultaneous alignment and folding of protein sequences. ( 0,744420092068033 )
Comput Math Methods Med - Identification of antioxidants from sequence information using na?ve Bayes. ( 0,744162043327584 )
Sci Data - Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus. ( 0,743688178419003 )
Med Biol Eng Comput - Enhanced spatio-temporal alignment of plantar pressure image sequences using B-splines. ( 0,74098730159828 )
Brief. Bioinformatics - Taxonomic binning of metagenome samples generated by next-generation sequencing technologies. ( 0,740191421077095 )
J. Comput. Biol. - Tracing the most parsimonious indel history. ( 0,73867743758907 )
Curr Protoc Bioinformatics - Using the RNAstructure Software Package to Predict Conserved RNA Structures. ( 0,736852668117208 )
Comput Biol Chem - Prediction of protein modification sites of gamma-carboxylation using position specific scoring matrices based evolutionary information. ( 0,736845278613349 )
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. ( 0,736342958924932 )
J Chem Inf Model - Protein secondary structure classification revisited: processing DSSP information with PSSC. ( 0,732787722711414 )
J Chem Inf Model - Improved helix and kink characterization in membrane proteins allows evaluation of kink sequence predictors. ( 0,730821909417891 )
J. Comput. Biol. - Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. ( 0,730170554814879 )
Comput. Biol. Med. - miRClassify: an advanced web server for miRNA family classification and annotation. ( 0,729999721016883 )
Sci Data - Comprehensive analysis of the venom gland transcriptome of the spider Dolomedes fimbriatus. ( 0,72979316499883 )
Brief. Bioinformatics - BamView: visualizing and interpretation of next-generation sequencing read alignments. ( 0,729737065900815 )
J. Comput. Biol. - Nonparametric combinatorial sequence models. ( 0,728639132172355 )
Comput Methods Programs Biomed - Protein secondary structure prediction using modular reciprocal bidirectional recurrent neural networks. ( 0,728394199747288 )
J Chem Inf Model - Parallel and antiparallel ?-strands differ in amino acid composition and availability of short constituent sequences. ( 0,727753480366567 )
Comput Biol Chem - A local average connectivity-based method for identifying essential proteins from the network level. ( 0,726589612852828 )
Comput. Biol. Med. - Remote protein homology detection and fold recognition using two-layer support vector machine classifiers. ( 0,725157571594899 )
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. ( 0,723280616054456 )
J Chem Inf Model - Comparative analysis of threshold and tessellation methods for determining protein contacts. ( 0,722233154916363 )
J. Comput. Biol. - Combinatorics of -structures. ( 0,717764404519119 )
Comput Math Methods Med - DV-curve representation of protein sequences and its application. ( 0,716918131861198 )
Comput Biol Chem - The challenge of annotating protein sequences: The tale of eight domains of unknown function in Pfam. ( 0,716516846638174 )
J. Comput. Biol. - ComB: SNP calling and mapping analysis for color and nucleotide space platforms. ( 0,71517938419422 )
Comput Biol Chem - Identification of putative and potential cross-reactive chickpea (Cicer arietinum) allergens through an in silico approach. ( 0,712877040860835 )
J. Comput. Biol. - Efficient traversal of beta-sheet protein folding pathways using ensemble models. ( 0,712022969147743 )
J. Comput. Biol. - Using structural and evolutionary information to detect and correct pyrosequencing errors in noncoding RNAs. ( 0,708814191828516 )
Comput. Biol. Med. - Remote homology detection incorporating the context of physicochemical properties. ( 0,708430926916008 )
Comput. Biol. Med. - New layers in understanding and predicting a-linolenic acid content in plants using amino acid characteristics of omega-3 fatty acid desaturase. ( 0,708083659931416 )
Brief. Bioinformatics - Base-calling for next-generation sequencing platforms. ( 0,706442608283421 )
Comput Biol Chem - Support vector machine with a Pearson VII function kernel for discriminating halophilic and non-halophilic proteins. ( 0,705240087222347 )
Comput. Biol. Med. - A content and structural assessment of oxidative motifs across a diverse set of life forms. ( 0,70495787933714 )
J Integr Bioinform - Exceptional single strand DNA word symmetry: analysis of evolutionary potentialities. ( 0,704123316787377 )
Brief. Bioinformatics - Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. ( 0,703816029592613 )
J Integr Bioinform - Predicting protein distance maps according to physicochemical properties. ( 0,703336974415913 )
Comput Biol Chem - Computational determination of the orientation of a heat repeat-like domain of DNA-PKcs. ( 0,700917376935014 )
Brief. Bioinformatics - A practical guide for the computational selection of residues to be experimentally characterized in protein families. ( 0,700887573136747 )
J. Comput. Biol. - Statistical significance of threading scores. ( 0,700643035023974 )
Brief. Bioinformatics - Ortholog identification in the presence of domain architecture rearrangement. ( 0,699729679763968 )
Comput Methods Programs Biomed - Discriminating protein structure classes by incorporating Pseudo Average Chemical Shift to Chou's general PseAAC and Support Vector Machine. ( 0,698765303140382 )
Comput Math Methods Med - Identification of DNA-binding proteins using support vector machine with sequence information. ( 0,698617967919288 )
Med Biol Eng Comput - Characterization and prediction of mRNA polyadenylation sites in human genes. ( 0,698480774303309 )
J. Comput. Biol. - Optimization of profile-to-profile alignment parameters for one-dimensional threading. ( 0,696787976550459 )
Comput Biol Chem - Multi-nucleation and vectorial folding pathways of large helix protein. ( 0,696715417893134 )
J. Comput. Biol. - Mapping reads on a genomic sequence: an algorithmic overview and a practical comparative analysis. ( 0,696217933177954 )
J Chem Inf Model - Protein structural statistics with PSS. ( 0,694861581918119 )
Comput Biol Chem - Identical sequence patterns in the ends of exons and introns of human protein-coding genes. ( 0,694245588340667 )
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. ( 0,692461835703736 )
Comput Biol Chem - A novel empirical mutual information approach to identify co-evolving amino acid positions of influenza A viruses. ( 0,687587256250072 )
Comput Biol Chem - Relationship between global structural parameters and Enzyme Commission hierarchy: implications for function prediction. ( 0,68751015159203 )
J. Comput. Biol. - Statistical significance of optical map alignments. ( 0,687007333019509 )
Comput Biol Chem - Genome-wide analysis and evolutionary study of sucrose non-fermenting 1-related protein kinase 2 (SnRK2) gene family members in Arabidopsis and Oryza. ( 0,685183006997763 )
Brief. Bioinformatics - Comparative genomics approach to detecting split-coding regions in a low-coverage genome: lessons from the chimaera Callorhinchus milii (Holocephali, Chondrichthyes). ( 0,685062768859333 )
J Biomed Inform - A similarity network approach for the analysis and comparison of protein sequence/structure sets. ( 0,684786217164338 )
J Chem Inf Model - Dihedral-based segment identification and classification of biopolymers I: proteins. ( 0,684071397872166 )
Comput. Biol. Med. - FRAN and RBF-PSO as two components of a hyper framework to recognize protein folds. ( 0,683753785197529 )
J. Comput. Biol. - Computational techniques for human genome resequencing using mated gapped reads. ( 0,68036319821995 )
Comput. Biol. Med. - Gene comparison based on the repetition of single-nucleotide structure patterns. ( 0,67892005974767 )
Comput Methods Programs Biomed - Sequence-based prediction of protein-binding sites in DNA: comparative study of two SVM models. ( 0,678507701646898 )
J Biomed Inform - A kinetic model-based algorithm to classify NGS short reads by their allele origin. ( 0,673256336586555 )
J. Comput. Biol. - Detection of structural variants involving repetitive regions in the reference genome. ( 0,669687858459794 )
Comput. Biol. Med. - Application of 2D graphic representation of protein sequence based on Huffman tree method. ( 0,66816013850415 )
Comput Biol Chem - Semantically predicting protein functions based on protein functional connectivity. ( 0,667612108117409 )
Brief. Bioinformatics - Ultrafast clustering algorithms for metagenomic sequence analysis. ( 0,667260193363108 )
Sci Data - Long-read, whole-genome shotgun sequence data for five model organisms. ( 0,665602381654235 )