Curr Protoc Bioinformatics - An Overview of RNA Sequence Analyses: Structure Prediction, ncRNA Gene Identification, and RNAi Design.

Tópicos

{ sequenc(1873) structur(1644) protein(1328) }
{ perform(1367) use(1326) method(1137) }
{ model(2656) set(1616) predict(1553) }
{ perform(999) metric(946) measur(919) }
{ first(2504) two(1366) second(1323) }
{ bind(1733) structur(1185) ligand(1036) }
{ motion(1329) object(1292) video(1091) }
{ model(2341) predict(2261) use(1141) }
{ state(1844) use(1261) util(961) }
{ model(3404) distribut(989) bayesian(671) }
{ measur(2081) correl(1212) valu(896) }
{ take(945) account(800) differ(722) }
{ framework(1458) process(801) describ(734) }
{ error(1145) method(1030) estim(1020) }
{ featur(1941) imag(1645) propos(1176) }
{ case(1353) use(1143) diagnosi(1136) }
{ import(1318) role(1303) understand(862) }
{ cost(1906) reduc(1198) effect(832) }
{ data(3008) multipl(1320) sourc(1022) }
{ can(774) often(719) complex(702) }
{ imag(1947) propos(1133) code(1026) }
{ data(1737) use(1416) pattern(1282) }
{ inform(2794) health(2639) internet(1427) }
{ system(1976) rule(880) can(841) }
{ imag(1057) registr(996) error(939) }
{ 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) }
{ patient(2315) diseas(1263) diabet(1191) }
{ studi(2440) review(1878) systemat(933) }
{ assess(1506) score(1403) qualiti(1306) }
{ treatment(1704) effect(941) patient(846) }
{ surgeri(1148) surgic(1085) robot(1054) }
{ problem(2511) optim(1539) algorithm(950) }
{ 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) }
{ method(1557) propos(1049) approach(1037) }
{ 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) }
{ general(901) number(790) one(736) }
{ method(984) reconstruct(947) comput(926) }
{ search(2224) databas(1162) retriev(909) }
{ howev(809) still(633) remain(590) }
{ 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) }
{ visual(1396) interact(850) tool(830) }
{ compound(1573) activ(1297) structur(1058) }
{ 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) }
{ monitor(1329) mobil(1314) devic(1160) }
{ ehr(2073) health(1662) electron(1139) }
{ research(1218) medic(880) student(794) }
{ patient(2837) hospit(1953) medic(668) }
{ data(2317) use(1299) case(1017) }
{ age(1611) year(1155) adult(843) }
{ medic(1828) order(1363) alert(1069) }
{ signal(2180) analysi(812) frequenc(800) }
{ group(2977) signific(1463) compar(1072) }
{ sampl(1606) size(1419) use(1276) }
{ gene(2352) biolog(1181) express(1162) }
{ 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) }
{ 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) }
{ 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) }
{ decis(3086) make(1611) patient(1517) }
{ process(1125) use(805) approach(778) }
{ activ(1452) weight(1219) physic(1104) }
{ method(1969) cluster(1462) data(1082) }
{ method(2212) result(1239) propos(1039) }
{ detect(2391) sensit(1101) algorithm(908) }

Resumo

This unit briefly describes the two fundamentally different methods for predicting RNA structures. The first is to find that structure with the minimum free energy of folding, as predicted by various thermodynamic parameters related to base-pair stacking, loop lengths, and other features. If one has only a single sequence, this thermodynamic approach is the best available method. The second fundamental approach to RNA structure prediction is to use multiple, homologous sequences for which one can infer a common structure, and then try and predict a structure common to all of the sequences. Such an approach is referred to as a comparative method or phylogenetic method of RNA structure prediction. Curr. Protoc. Bioinform. 43:12.1.1-12.1.3. ? 2013 by John Wiley & Sons, Inc.

Resumo Limpo

unit briefli describ two fundament differ method predict rna structur first find structur minimum free energi fold predict various thermodynam paramet relat basepair stack loop length featur one singl sequenc thermodynam approach best avail method second fundament approach rna structur predict use multipl homolog sequenc one can infer common structur tri predict structur common sequenc approach refer compar method phylogenet method rna structur predict curr protoc bioinform john wiley son inc

Resumos Similares

Comput Math Methods Med - DV-curve representation of protein sequences and its application. ( 0,795710261253228 )
Comput Biol Chem - Statistical analysis and exposure status classification of transmembrane beta barrel residues. ( 0,777803551835395 )
Curr Protoc Bioinformatics - Using the RNAstructure Software Package to Predict Conserved RNA Structures. ( 0,747428236108851 )
J Chem Inf Model - Protein secondary structure prediction with SPARROW. ( 0,745041618098348 )
Comput Methods Programs Biomed - Sequence-based prediction of protein-binding sites in DNA: comparative study of two SVM models. ( 0,744277043648293 )
Comput Biol Chem - ProSTRIP: A method to find similar structural repeats in three-dimensional protein structures. ( 0,741535207428516 )
Comput Biol Chem - ProCoCoA: A quantitative approach for analyzing protein core composition. ( 0,737133639959924 )
Comput Biol Chem - Multi-nucleation and vectorial folding pathways of large helix protein. ( 0,726566148810022 )
Comput Biol Chem - Analysis of sequence repeats of proteins in the PDB. ( 0,723976341801234 )
J Chem Inf Model - Data-driven high-throughput prediction of the 3-D structure of small molecules: review and progress. ( 0,723569070488821 )
Comput Biol Chem - Protein fold recognition based on functional domain composition. ( 0,72050297859776 )
J Chem Inf Model - Tertiary structure prediction of RNA-RNA complexes using a secondary structure and fragment-based method. ( 0,717664743959053 )
J. Comput. Biol. - Accurate mass spectrometry based protein quantification via shared peptides. ( 0,713670332428143 )
Brief. Bioinformatics - De novo assembly of short sequence reads. ( 0,711267791335394 )
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. ( 0,71122071922776 )
J. Comput. Biol. - Evaluating, comparing, and interpreting protein domain hierarchies. ( 0,710234111384071 )
J. Comput. Biol. - Mapping reads on a genomic sequence: an algorithmic overview and a practical comparative analysis. ( 0,703738014956397 )
Comput Biol Chem - Bacterial protein structures reveal phylum dependent divergence. ( 0,703344962600816 )
J. Comput. Biol. - Simultaneous alignment and folding of protein sequences. ( 0,70270295333582 )
J Integr Bioinform - Predicting protein distance maps according to physicochemical properties. ( 0,702160070766319 )
Comput Biol Chem - Characterizing regions in the human genome unmappable by next-generation-sequencing at the read length of 1000 bases. ( 0,70212073126324 )
Comput Methods Programs Biomed - Protein secondary structure prediction using modular reciprocal bidirectional recurrent neural networks. ( 0,701615575878308 )
J Chem Inf Model - Improved helix and kink characterization in membrane proteins allows evaluation of kink sequence predictors. ( 0,70037982644519 )
Comput. Biol. Med. - An insight into the molecular basis for convergent evolution in fish antifreeze Proteins. ( 0,698801277335501 )
Comput Biol Chem - The frequency of poly(G) tracts in the human genome and their use as a sensor of DNA damage. ( 0,693530276698375 )
Comput. Biol. Med. - Improving protein secondary structure prediction using a multi-modal BP method. ( 0,689413353754735 )
J Chem Inf Model - Protein secondary structure classification revisited: processing DSSP information with PSSC. ( 0,689038597418435 )
Comput Math Methods Med - Quad-PRE: a hybrid method to predict protein quaternary structure attributes. ( 0,688117410344252 )
Comput Biol Chem - Human-chimpanzee alignment: ortholog exponentials and paralog power laws. ( 0,688034524027838 )
BMC Med Inform Decis Mak - Efficient protein structure search using indexing methods. ( 0,687229984378957 )
J Chem Inf Model - ProBiS-database: precalculated binding site similarities and local pairwise alignments of PDB structures. ( 0,686817410424677 )
Brief. Bioinformatics - New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing. ( 0,685470221119744 )
Comput Biol Chem - A novel empirical mutual information approach to identify co-evolving amino acid positions of influenza A viruses. ( 0,681377013043583 )
J. Comput. Biol. - ComB: SNP calling and mapping analysis for color and nucleotide space platforms. ( 0,681071896999316 )
J. Comput. Biol. - Combinatorics of -structures. ( 0,680959627417345 )
J. Comput. Biol. - Optimization of profile-to-profile alignment parameters for one-dimensional threading. ( 0,680537692760391 )
Comput Biol Chem - Computational insight into nitration of human myoglobin. ( 0,68036800295516 )
Comput. Biol. Med. - Remote homology detection incorporating the context of physicochemical properties. ( 0,679575840843478 )
Comput Biol Chem - Direct correlation analysis improves fold recognition. ( 0,679541842648159 )
Comput Biol Chem - Identification of putative and potential cross-reactive chickpea (Cicer arietinum) allergens through an in silico approach. ( 0,678728667524332 )
Comput. Biol. Med. - Prediction of protein functions based on function-function correlation relations. ( 0,67797733378277 )
Med Biol Eng Comput - Enhanced spatio-temporal alignment of plantar pressure image sequences using B-splines. ( 0,677837595400774 )
J. Comput. Biol. - Nonparametric combinatorial sequence models. ( 0,677248476997929 )
J Chem Inf Model - PocketAlign a novel algorithm for aligning binding sites in protein structures. ( 0,676687971515875 )
Comput Biol Chem - The challenge of annotating protein sequences: The tale of eight domains of unknown function in Pfam. ( 0,674141860717487 )
J Integr Bioinform - Prediction of thioredoxin and glutaredoxin target proteins by identifying reversibly oxidized cysteinyl residues. ( 0,67360743489881 )
Comput. Biol. Med. - miRClassify: an advanced web server for miRNA family classification and annotation. ( 0,671345016158653 )
J Chem Inf Model - Comparative analysis of threshold and tessellation methods for determining protein contacts. ( 0,670127337842744 )
J Chem Inf Model - Protein structural statistics with PSS. ( 0,669233320378411 )
Brief. Bioinformatics - Taxonomic binning of metagenome samples generated by next-generation sequencing technologies. ( 0,667510015095777 )
J. Comput. Biol. - AREM: aligning short reads from ChIP-sequencing by expectation maximization. ( 0,666527958690873 )
J. Comput. Biol. - Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. ( 0,664459244225678 )
J. Comput. Biol. - Statistical significance of optical map alignments. ( 0,663700711271721 )
Comput Biol Chem - Identical sequence patterns in the ends of exons and introns of human protein-coding genes. ( 0,663144860252287 )
J Chem Inf Model - Modules identification in protein structures: the topological and geometrical solutions. ( 0,662163409779798 )
Comput Biol Chem - A local average connectivity-based method for identifying essential proteins from the network level. ( 0,661759013655266 )
Brief. Bioinformatics - Systematic identification of Class I HDAC substrates. ( 0,661265575285822 )
Comput. Biol. Med. - Structural alphabet motif discovery and a structural motif database. ( 0,659127046121971 )
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. ( 0,657400626996387 )
Brief. Bioinformatics - Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. ( 0,656500936095863 )
J. Comput. Biol. - Sequence alignment of viral channel proteins with cellular ion channels. ( 0,656089594296525 )
J Chem Inf Model - Kink characterization and modeling in transmembrane protein structures. ( 0,654982977739207 )
Brief. Bioinformatics - A practical guide for the computational selection of residues to be experimentally characterized in protein families. ( 0,654718216519958 )
J Integr Bioinform - Exceptional single strand DNA word symmetry: analysis of evolutionary potentialities. ( 0,650432581745275 )
J Integr Bioinform - A hierarchical approach to protein fold prediction. ( 0,649575040906657 )
J. Comput. Biol. - Optimization of combinatorial mutagenesis. ( 0,649091807896299 )
Comput Biol Chem - Support vector machine with a Pearson VII function kernel for discriminating halophilic and non-halophilic proteins. ( 0,647804285106459 )
Comput. Biol. Med. - A content and structural assessment of oxidative motifs across a diverse set of life forms. ( 0,646852116577339 )
Comput. Biol. Med. - A context evaluation approach for structural comparison of proteins using cross entropy over n-gram modelling. ( 0,645851487388685 )
J Chem Inf Model - Parallel and antiparallel ?-strands differ in amino acid composition and availability of short constituent sequences. ( 0,645620136971875 )
Comput. Biol. Med. - Application of 2D graphic representation of protein sequence based on Huffman tree method. ( 0,642009408596211 )
IEEE Trans Image Process - Pattern masking estimation in image with structural uncertainty. ( 0,641158226323998 )
Comput Biol Chem - Identification and characterization of lysine-methylated sites on histones and non-histone proteins. ( 0,63850237613661 )
Comput Biol Chem - Gene cloning, homology comparison and analysis of the main functional structure domains of beta estrogen receptor in Jining Gray goat. ( 0,638458823771061 )
J. Comput. Biol. - Statistical significance of threading scores. ( 0,637434678342221 )
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. ( 0,637004089443112 )
Brief. Bioinformatics - Ortholog identification in the presence of domain architecture rearrangement. ( 0,636629751089873 )
Sci Data - Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus. ( 0,636618002597985 )
Curr Protoc Bioinformatics - Comparative Protein Structure Modeling Using MODELLER. ( 0,63552381923334 )
J. Comput. Biol. - Statistical significance of normalized global alignment. ( 0,63212426679704 )
Comput. Biol. Med. - Signal peptide discrimination and cleavage site identification using SVM and NN. ( 0,631010665248441 )
Comput Biol Chem - Predicting protein-RNA interaction amino acids using random forest based on submodularity subset selection. ( 0,629908140894609 )
Sci Data - Long-read, whole-genome shotgun sequence data for five model organisms. ( 0,628358204500202 )
J. Comput. Biol. - Efficient traversal of beta-sheet protein folding pathways using ensemble models. ( 0,625955166229206 )
Sci Data - Comprehensive analysis of the venom gland transcriptome of the spider Dolomedes fimbriatus. ( 0,625352417568186 )
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. ( 0,625346658508142 )
J Chem Inf Model - Dihedral-based segment identification and classification of biopolymers II: polynucleotides. ( 0,625257356196069 )
J. Comput. Biol. - IDBA-MTP: A Hybrid Metatranscriptomic Assembler Based on Protein Information. ( 0,623386355214004 )
Brief. Bioinformatics - Comparative genomics approach to detecting split-coding regions in a low-coverage genome: lessons from the chimaera Callorhinchus milii (Holocephali, Chondrichthyes). ( 0,619100714618738 )
Brief. Bioinformatics - Base-calling for next-generation sequencing platforms. ( 0,618798345509313 )
Comput Biol Chem - Investigating long range correlation in DNA sequences using significance tests of conditional mutual information. ( 0,617421631414643 )
Comput Biol Chem - Computational determination of the orientation of a heat repeat-like domain of DNA-PKcs. ( 0,616364391647619 )
J. Comput. Biol. - A novel technique for detecting putative horizontal gene transfer in the sequence space. ( 0,615346936996547 )
Brief. Bioinformatics - Identify drug repurposing candidates by mining the protein data bank. ( 0,615074845633667 )
Comput Biol Chem - A balance-evolution artificial bee colony algorithm for protein structure optimization based on a three-dimensional AB off-lattice model. ( 0,615070464121042 )
Comput Math Methods Med - Na?ve Bayes classifier with feature selection to identify phage virion proteins. ( 0,614701185702871 )
J Biomed Inform - A similarity network approach for the analysis and comparison of protein sequence/structure sets. ( 0,613376710547548 )
Comput. Biol. Med. - Improving protein complex classification accuracy using amino acid composition profile. ( 0,609838665579596 )
J. Comput. Biol. - Reconstructing the history of large-scale genomic changes: biological questions and computational challenges. ( 0,609507059000499 )
J Chem Inf Model - Context-based features enhance protein secondary structure prediction accuracy. ( 0,609268119678694 )