Brief. Bioinformatics - Ortholog identification in the presence of domain architecture rearrangement.

Tópicos

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

Resumo

Ortholog identification is used in gene functional annotation, species phylogeny estimation, phylogenetic profile construction and many other analyses. Bioinformatics methods for ortholog identification are commonly based on pairwise protein sequence comparisons between whole genomes. Phylogenetic methods of ortholog identification have also been developed; these methods can be applied to protein data sets sharing a common domain architecture or which share a single functional domain but differ outside this region of homology. While promiscuous domains represent a challenge to all orthology prediction methods, overall structural similarity is highly correlated with proximity in a phylogenetic tree, conferring a degree of robustness to phylogenetic methods. In this article, we review the issues involved in orthology prediction when data sets include sequences with structurally heterogeneous domain architectures, with particular attention to automated methods designed for high-throughput application, and present a case study to illustrate the challenges in this area.

Resumo Limpo

ortholog identif use gene function annot speci phylogeni estim phylogenet profil construct mani analys bioinformat method ortholog identif common base pairwis protein sequenc comparison whole genom phylogenet method ortholog identif also develop method can appli protein data set share common domain architectur share singl function domain differ outsid region homolog promiscu domain repres challeng ortholog predict method overal structur similar high correl proxim phylogenet tree confer degre robust phylogenet method articl review issu involv ortholog predict data set includ sequenc structur heterogen domain architectur particular attent autom method design highthroughput applic present case studi illustr challeng area

Resumos Similares

J Chem Inf Model - Improved helix and kink characterization in membrane proteins allows evaluation of kink sequence predictors. ( 0,791722360919188 )
Comput Biol Chem - The frequency of poly(G) tracts in the human genome and their use as a sensor of DNA damage. ( 0,786820008143079 )
Brief. Bioinformatics - De novo assembly of short sequence reads. ( 0,786437661138049 )
J Chem Inf Model - Protein structural statistics with PSS. ( 0,778848435370864 )
J Chem Inf Model - Parallel and antiparallel ?-strands differ in amino acid composition and availability of short constituent sequences. ( 0,776557794268924 )
J. Comput. Biol. - ComB: SNP calling and mapping analysis for color and nucleotide space platforms. ( 0,776406668712833 )
Comput Methods Programs Biomed - Can computational biology improve the phylogenetic analysis of insulin? ( 0,775584860731276 )
Comput Biol Chem - Computational insight into nitration of human myoglobin. ( 0,772611572161428 )
J Chem Inf Model - Comparative analysis of threshold and tessellation methods for determining protein contacts. ( 0,77174501854188 )
Comput Biol Chem - Analysis of sequence repeats of proteins in the PDB. ( 0,764603105731872 )
Sci Data - Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus. ( 0,760179943489311 )
Comput Biol Chem - Statistical analysis and exposure status classification of transmembrane beta barrel residues. ( 0,759717747408695 )
Brief. Bioinformatics - New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing. ( 0,757621958096605 )
J Chem Inf Model - Modules identification in protein structures: the topological and geometrical solutions. ( 0,757412154025769 )
J Chem Inf Model - Protein secondary structure prediction with SPARROW. ( 0,756833302082898 )
J. Comput. Biol. - Evaluating, comparing, and interpreting protein domain hierarchies. ( 0,756477328542591 )
Comput Biol Chem - ProSTRIP: A method to find similar structural repeats in three-dimensional protein structures. ( 0,756187068024453 )
Comput Biol Chem - Protein fold recognition based on functional domain composition. ( 0,755522182474403 )
Comput Biol Chem - Characterizing regions in the human genome unmappable by next-generation-sequencing at the read length of 1000 bases. ( 0,749695182498312 )
Comput Biol Chem - A novel empirical mutual information approach to identify co-evolving amino acid positions of influenza A viruses. ( 0,749248575771142 )
Comput Biol Chem - Bacterial protein structures reveal phylum dependent divergence. ( 0,748789929203984 )
Comput Math Methods Med - DV-curve representation of protein sequences and its application. ( 0,748575743211924 )
J Chem Inf Model - ProBiS-database: precalculated binding site similarities and local pairwise alignments of PDB structures. ( 0,748387208832102 )
J. Comput. Biol. - Nonparametric combinatorial sequence models. ( 0,746981330873026 )
Comput. Biol. Med. - miRClassify: an advanced web server for miRNA family classification and annotation. ( 0,746187935714599 )
J Chem Inf Model - Tertiary structure prediction of RNA-RNA complexes using a secondary structure and fragment-based method. ( 0,743918928230869 )
Comput Biol Chem - Identification and characterization of lysine-methylated sites on histones and non-histone proteins. ( 0,743061374083481 )
J Chem Inf Model - Protein secondary structure classification revisited: processing DSSP information with PSSC. ( 0,742165857061199 )
J Chem Inf Model - Kink characterization and modeling in transmembrane protein structures. ( 0,741223169348978 )
Comput Biol Chem - A local average connectivity-based method for identifying essential proteins from the network level. ( 0,739658344701497 )
Brief. Bioinformatics - Taxonomic binning of metagenome samples generated by next-generation sequencing technologies. ( 0,739047284487065 )
Brief. Bioinformatics - Systematic identification of Class I HDAC substrates. ( 0,738545750617101 )
Brief. Bioinformatics - BamView: visualizing and interpretation of next-generation sequencing read alignments. ( 0,738521907727426 )
J. Comput. Biol. - Optimization of profile-to-profile alignment parameters for one-dimensional threading. ( 0,737586307910765 )
Comput Biol Chem - ProCoCoA: A quantitative approach for analyzing protein core composition. ( 0,73481398624966 )
Comput. Biol. Med. - Improving protein secondary structure prediction using a multi-modal BP method. ( 0,734216074222865 )
Comput. Biol. Med. - An insight into the molecular basis for convergent evolution in fish antifreeze Proteins. ( 0,733018730991567 )
Comput Biol Chem - The challenge of annotating protein sequences: The tale of eight domains of unknown function in Pfam. ( 0,732406069899455 )
Comput Biol Chem - Human-chimpanzee alignment: ortholog exponentials and paralog power laws. ( 0,732125065276047 )
J. Comput. Biol. - Computational techniques for human genome resequencing using mated gapped reads. ( 0,732053358954475 )
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. ( 0,73169143932115 )
Brief. Bioinformatics - Sequencing technologies and tools for short tandem repeat variation detection. ( 0,731386592907918 )
J. Comput. Biol. - Efficient traversal of beta-sheet protein folding pathways using ensemble models. ( 0,72781253777691 )
J. Comput. Biol. - Simultaneous alignment and folding of protein sequences. ( 0,725500261845627 )
Comput Biol Chem - Multi-nucleation and vectorial folding pathways of large helix protein. ( 0,72222436689263 )
Sci Data - A draft genome for the African crocodilian trypanosome Trypanosoma grayi. ( 0,721261886006388 )
Brief. Bioinformatics - A practical guide for the computational selection of residues to be experimentally characterized in protein families. ( 0,720462647367003 )
Comput Math Methods Med - Quad-PRE: a hybrid method to predict protein quaternary structure attributes. ( 0,720255719505992 )
Comput Biol Chem - Identification of putative and potential cross-reactive chickpea (Cicer arietinum) allergens through an in silico approach. ( 0,719428200907712 )
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. ( 0,718735519446036 )
J. Comput. Biol. - Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. ( 0,718019675918125 )
J Chem Inf Model - MetalS2: a tool for the structural alignment of minimal functional sites in metal-binding proteins and nucleic acids. ( 0,71707142456321 )
J. Comput. Biol. - Combinatorics of -structures. ( 0,714029115685219 )
Brief. Bioinformatics - Automated glycopeptide analysis--review of current state and future directions. ( 0,713813537273861 )
Comput Math Methods Med - ProBLM web server: protein and membrane placement and orientation package. ( 0,707430435949566 )
Comput. Biol. Med. - A context evaluation approach for structural comparison of proteins using cross entropy over n-gram modelling. ( 0,707169704901596 )
Brief. Bioinformatics - Bioinformatics tools and challenges in structural analysis of lipidomics MS/MS data. ( 0,706385758483291 )
Brief. Bioinformatics - Base-calling for next-generation sequencing platforms. ( 0,706324638017148 )
Med Biol Eng Comput - Enhanced spatio-temporal alignment of plantar pressure image sequences using B-splines. ( 0,704642319121564 )
Comput Biol Chem - Identical sequence patterns in the ends of exons and introns of human protein-coding genes. ( 0,700986774374859 )
Comput. Biol. Med. - Prediction of protein functions based on function-function correlation relations. ( 0,700556693241074 )
Curr Protoc Bioinformatics - Using the RNAstructure Software Package to Predict Conserved RNA Structures. ( 0,700026297125299 )
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. ( 0,699986336400069 )
Comput. Biol. Med. - Intron identification approaches based on weighted features and fuzzy decision trees. ( 0,699729679763968 )
Comput. Biol. Med. - A content and structural assessment of oxidative motifs across a diverse set of life forms. ( 0,698576800244812 )
J Integr Bioinform - Complementarity of network and sequence information in homologous proteins. ( 0,698296115374781 )
J. Comput. Biol. - AREM: aligning short reads from ChIP-sequencing by expectation maximization. ( 0,69416918643765 )
Brief. Bioinformatics - Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. ( 0,693357531433019 )
Brief. Bioinformatics - Comparative genomics approach to detecting split-coding regions in a low-coverage genome: lessons from the chimaera Callorhinchus milii (Holocephali, Chondrichthyes). ( 0,692852210450836 )
Comput. Biol. Med. - Signal peptide discrimination and cleavage site identification using SVM and NN. ( 0,692570965630824 )
BMC Med Inform Decis Mak - Efficient protein structure search using indexing methods. ( 0,692130090636275 )
Brief. Bioinformatics - Congruency in the prediction of pathogenic missense mutations: state-of-the-art web-based tools. ( 0,691207604855109 )
Comput. Biol. Med. - Remote protein homology detection and fold recognition using two-layer support vector machine classifiers. ( 0,689151385205363 )
Comput Biol Chem - Comparison of linear gap penalties and profile-based variable gap penalties in profile-profile alignments. ( 0,688668359058612 )
Comput Biol Chem - Error compensation of tRNA misacylation by codon-anticodon mismatch prevents translational amino acid misinsertion. ( 0,688506511771819 )
Comput Biol Chem - Computational determination of the orientation of a heat repeat-like domain of DNA-PKcs. ( 0,688225768567393 )
J. Comput. Biol. - Statistical significance of threading scores. ( 0,688186230132376 )
Comput. Biol. Med. - Application of 2D graphic representation of protein sequence based on Huffman tree method. ( 0,687576192425898 )
Comput. Biol. Med. - LRRsearch: An asynchronous server-based application for the prediction of leucine-rich repeat motifs and an integrative database of NOD-like receptors. ( 0,686001346068234 )
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. ( 0,685885246512227 )
J. Comput. Biol. - IDBA-MTP: A Hybrid Metatranscriptomic Assembler Based on Protein Information. ( 0,685319593223702 )
Comput Biol Chem - Distribution of N-glycosylation sequons in proteins: how apart are they? ( 0,685022561235642 )
J Integr Bioinform - Exceptional single strand DNA word symmetry: analysis of evolutionary potentialities. ( 0,682828079605201 )
J Chem Inf Model - Dihedral-based segment identification and classification of biopolymers I: proteins. ( 0,680677198775257 )
Sci Data - Long-read, whole-genome shotgun sequence data for five model organisms. ( 0,680362543812271 )
J Chem Inf Model - Dihedral-based segment identification and classification of biopolymers II: polynucleotides. ( 0,678152915056213 )
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. ( 0,677489232409647 )
Comput Methods Programs Biomed - Protein secondary structure prediction using modular reciprocal bidirectional recurrent neural networks. ( 0,677052482501541 )
Comput. Biol. Med. - The possible role of HSPs on Beh?et's disease: a bioinformatic approach. ( 0,675501590026471 )
Sci Data - Comprehensive analysis of the venom gland transcriptome of the spider Dolomedes fimbriatus. ( 0,67493138973755 )
J. Comput. Biol. - A novel technique for detecting putative horizontal gene transfer in the sequence space. ( 0,67314635516179 )
J Integr Bioinform - A hierarchical approach to protein fold prediction. ( 0,671935398105757 )
J. Comput. Biol. - Statistical significance of optical map alignments. ( 0,670915375805898 )
Comput Biol Chem - Predicting protein-protein interactions using graph invariants and a neural network. ( 0,669329771903467 )
J. Comput. Biol. - Mapping reads on a genomic sequence: an algorithmic overview and a practical comparative analysis. ( 0,668463959119472 )
J. Comput. Biol. - The generating function approach for Peptide identification in spectral networks. ( 0,667124316852553 )
Comput Math Methods Med - Identification of antioxidants from sequence information using na?ve Bayes. ( 0,664855452346031 )
Curr Protoc Bioinformatics - Comparative Protein Structure Modeling Using MODELLER. ( 0,658160867761687 )
Comput Biol Chem - Investigating long range correlation in DNA sequences using significance tests of conditional mutual information. ( 0,658003451396644 )
J Chem Inf Model - PocketAlign a novel algorithm for aligning binding sites in protein structures. ( 0,655217978778198 )