Comput. Biol. Med. - Haemophilus influenzae Genome Database (HIGDB): a single point web resource for Haemophilus influenzae.

Tópicos

{ sequenc(1873) structur(1644) protein(1328) }
{ data(3963) clinic(1234) research(1004) }
{ general(901) number(790) one(736) }
{ search(2224) databas(1162) retriev(909) }
{ patient(2315) diseas(1263) diabet(1191) }
{ studi(2440) review(1878) systemat(933) }
{ framework(1458) process(801) describ(734) }
{ system(1050) medic(1026) inform(1018) }
{ gene(2352) biolog(1181) express(1162) }
{ patient(1821) servic(1111) care(1106) }
{ survey(1388) particip(1329) question(1065) }
{ method(2212) result(1239) propos(1039) }
{ data(1737) use(1416) pattern(1282) }
{ method(1219) similar(1157) match(930) }
{ featur(3375) classif(2383) classifi(1994) }
{ design(1359) user(1324) use(1319) }
{ control(1307) perform(991) simul(935) }
{ method(984) reconstruct(947) comput(926) }
{ risk(3053) factor(974) diseas(938) }
{ health(3367) inform(1360) care(1135) }
{ monitor(1329) mobil(1314) devic(1160) }
{ state(1844) use(1261) util(961) }
{ data(3008) multipl(1320) sourc(1022) }
{ first(2504) two(1366) second(1323) }
{ analysi(2126) use(1163) compon(1037) }
{ use(976) code(926) identifi(902) }
{ model(3404) distribut(989) bayesian(671) }
{ can(774) often(719) complex(702) }
{ imag(1947) propos(1133) code(1026) }
{ 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) }
{ imag(2830) propos(1344) filter(1198) }
{ network(2748) neural(1063) input(814) }
{ imag(2675) segment(2577) method(1081) }
{ take(945) account(800) differ(722) }
{ motion(1329) object(1292) video(1091) }
{ assess(1506) score(1403) qualiti(1306) }
{ treatment(1704) effect(941) patient(846) }
{ surgeri(1148) surgic(1085) robot(1054) }
{ 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) }
{ 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) }
{ model(2220) cell(1177) simul(1124) }
{ care(1570) inform(1187) nurs(1089) }
{ featur(1941) imag(1645) propos(1176) }
{ case(1353) use(1143) diagnosi(1136) }
{ howev(809) still(633) remain(590) }
{ studi(1410) differ(1259) use(1210) }
{ perform(999) metric(946) measur(919) }
{ 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) }
{ spatial(1525) area(1432) region(1030) }
{ record(1888) medic(1808) patient(1693) }
{ model(3480) simul(1196) paramet(876) }
{ ehr(2073) health(1662) electron(1139) }
{ 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) }
{ signal(2180) analysi(812) frequenc(800) }
{ cost(1906) reduc(1198) effect(832) }
{ group(2977) signific(1463) compar(1072) }
{ sampl(1606) size(1419) use(1276) }
{ intervent(3218) particip(2042) group(1664) }
{ activ(1138) subject(705) human(624) }
{ time(1939) patient(1703) rate(768) }
{ use(2086) technolog(871) perceiv(783) }
{ can(981) present(881) function(850) }
{ 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(1733) differ(960) four(931) }
{ drug(1928) target(777) effect(648) }
{ result(1111) use(1088) new(759) }
{ implement(1333) system(1263) develop(1122) }
{ 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) }
{ detect(2391) sensit(1101) algorithm(908) }

Resumo

CKGROUND: Haemophilus influenzae (H. Influenzae) is the causative agent of pneumonia, bacteraemia and meningitis. The organism is responsible for large number of deaths in both developed and developing countries. Even-though the first bacterial genome to be sequenced was that of H. Influenzae, there is no exclusive database dedicated for H. Influenzae. This prompted us to develop the Haemophilus influenzae Genome Database (HIGDB).METHODS: All data of HIGDB are stored and managed in MySQL database. The HIGDB is hosted on Solaris server and developed using PERL modules. Ajax and JavaScript are used for the interface development.RESULTS: The HIGDB contains detailed information on 42,741 proteins, 18,077 genes including 10 whole genome sequences and also 284 three dimensional structures of proteins of H. influenzae. In addition, the database provides "Motif search" and "GBrowse". The HIGDB is freely accessible through the URL: http://bioserver1.physics.iisc.ernet.in/HIGDB/.DISCUSSION: The HIGDB will be a single point access for bacteriological, clinical, genomic and proteomic information of H. influenzae. The database can also be used to identify DNA motifs within H. influenzae genomes and to compare gene or protein sequences of a particular strain with other strains of H. influenzae.

Resumo Limpo

ckground haemophilus influenza h influenza causat agent pneumonia bacteraemia mening organ respons larg number death develop develop countri eventhough first bacteri genom sequenc h influenza exclus databas dedic h influenza prompt us develop haemophilus influenza genom databas higdbmethod data higdb store manag mysql databas higdb host solari server develop use perl modul ajax javascript use interfac developmentresult higdb contain detail inform protein gene includ whole genom sequenc also three dimension structur protein h influenza addit databas provid motif search gbrows higdb freeli access url httpbioserverphysicsiiscernetinhigdbdiscuss higdb will singl point access bacteriolog clinic genom proteom inform h influenza databas can also use identifi dna motif within h influenza genom compar gene protein sequenc particular strain strain h influenza

Resumos Similares

Brief. Bioinformatics - New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing. ( 0,78743961352657 )
Comput Biol Chem - Characterizing regions in the human genome unmappable by next-generation-sequencing at the read length of 1000 bases. ( 0,771280099885631 )
J. Comput. Biol. - IDBA-MTP: A Hybrid Metatranscriptomic Assembler Based on Protein Information. ( 0,754430702084877 )
Comput Biol Chem - ProSTRIP: A method to find similar structural repeats in three-dimensional protein structures. ( 0,74703557312253 )
Brief. Bioinformatics - De novo assembly of short sequence reads. ( 0,74418415160227 )
J Chem Inf Model - ProBiS-database: precalculated binding site similarities and local pairwise alignments of PDB structures. ( 0,736256552288852 )
Comput Biol Chem - Bacterial protein structures reveal phylum dependent divergence. ( 0,735055665818427 )
Comput. Biol. Med. - Application of 2D graphic representation of protein sequence based on Huffman tree method. ( 0,730575887773073 )
Brief. Bioinformatics - Taxonomic binning of metagenome samples generated by next-generation sequencing technologies. ( 0,719635070585765 )
Comput Biol Chem - Analysis of sequence repeats of proteins in the PDB. ( 0,71954828269032 )
Comput. Biol. Med. - An insight into the molecular basis for convergent evolution in fish antifreeze Proteins. ( 0,715556080661616 )
J Chem Inf Model - Context-based features enhance protein secondary structure prediction accuracy. ( 0,715217593267893 )
Comput Biol Chem - The frequency of poly(G) tracts in the human genome and their use as a sensor of DNA damage. ( 0,71517908303228 )
Comput Biol Chem - Computational determination of the orientation of a heat repeat-like domain of DNA-PKcs. ( 0,712949210217324 )
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. ( 0,710371255688717 )
Comput Biol Chem - Identification of putative and potential cross-reactive chickpea (Cicer arietinum) allergens through an in silico approach. ( 0,710369027140431 )
Comput. Biol. Med. - miRClassify: an advanced web server for miRNA family classification and annotation. ( 0,709193868977254 )
J Chem Inf Model - Tertiary structure prediction of RNA-RNA complexes using a secondary structure and fragment-based method. ( 0,708749307862342 )
Comput Biol Chem - Statistical analysis and exposure status classification of transmembrane beta barrel residues. ( 0,708290170706672 )
Sci Data - Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus. ( 0,706582907195926 )
Comput Biol Chem - The challenge of annotating protein sequences: The tale of eight domains of unknown function in Pfam. ( 0,705820836217161 )
BMC Med Inform Decis Mak - Efficient protein structure search using indexing methods. ( 0,705405479618715 )
Brief. Bioinformatics - Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. ( 0,702462750140406 )
J Chem Inf Model - Protein secondary structure prediction with SPARROW. ( 0,699225284230073 )
J. Comput. Biol. - Nonparametric combinatorial sequence models. ( 0,695909411273963 )
J Integr Bioinform - Predicting protein distance maps according to physicochemical properties. ( 0,693505924335432 )
Comput Math Methods Med - Quad-PRE: a hybrid method to predict protein quaternary structure attributes. ( 0,69242367344914 )
Comput Biol Chem - Human-chimpanzee alignment: ortholog exponentials and paralog power laws. ( 0,692307692307692 )
Brief. Bioinformatics - Three-stage quality control strategies for DNA re-sequencing data. ( 0,691269868717276 )
Comput Biol Chem - ProCoCoA: A quantitative approach for analyzing protein core composition. ( 0,685517491211794 )
Brief. Bioinformatics - Systematic identification of Class I HDAC substrates. ( 0,68475227121768 )
Comput. Biol. Med. - Improving protein secondary structure prediction using a multi-modal BP method. ( 0,682535445321057 )
Comput. Biol. Med. - A content and structural assessment of oxidative motifs across a diverse set of life forms. ( 0,681863300111118 )
Comput Biol Chem - Multi-nucleation and vectorial folding pathways of large helix protein. ( 0,67977486185934 )
Sci Data - Comprehensive analysis of the venom gland transcriptome of the spider Dolomedes fimbriatus. ( 0,679029146690167 )
Comput Biol Chem - Protein fold recognition based on functional domain composition. ( 0,677678829234912 )
Comput Biol Chem - Computational insight into nitration of human myoglobin. ( 0,676908791240322 )
Comput. Biol. Med. - A context evaluation approach for structural comparison of proteins using cross entropy over n-gram modelling. ( 0,673676419262942 )
J. Comput. Biol. - Evaluating, comparing, and interpreting protein domain hierarchies. ( 0,673283486527871 )
Brief. Bioinformatics - A practical guide for the computational selection of residues to be experimentally characterized in protein families. ( 0,672640132419553 )
J. Comput. Biol. - Mapping reads on a genomic sequence: an algorithmic overview and a practical comparative analysis. ( 0,670444113829955 )
J. Comput. Biol. - Simultaneous alignment and folding of protein sequences. ( 0,670400919677688 )
Comput. Biol. Med. - Predicting protein-binding RNA nucleotides using the feature-based removal of data redundancy and the interaction propensity of nucleotide triplets. ( 0,669490634192203 )
Curr Protoc Bioinformatics - Using SOAPaligner for Short Reads Alignment. ( 0,668360989795146 )
J Chem Inf Model - Improved helix and kink characterization in membrane proteins allows evaluation of kink sequence predictors. ( 0,668337254963562 )
J Chem Inf Model - Modules identification in protein structures: the topological and geometrical solutions. ( 0,667590478557022 )
J Chem Inf Model - Parallel and antiparallel ?-strands differ in amino acid composition and availability of short constituent sequences. ( 0,666684789332723 )
Curr Protoc Bioinformatics - Using the RNAstructure Software Package to Predict Conserved RNA Structures. ( 0,664464352522575 )
J. Comput. Biol. - Sequence alignment of viral channel proteins with cellular ion channels. ( 0,66437233454417 )
J Chem Inf Model - Comparative analysis of threshold and tessellation methods for determining protein contacts. ( 0,66310104141553 )
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. ( 0,662736946578435 )
J. Comput. Biol. - ComB: SNP calling and mapping analysis for color and nucleotide space platforms. ( 0,66082930935635 )
Comput Biol Chem - Identical sequence patterns in the ends of exons and introns of human protein-coding genes. ( 0,659542051790455 )
J Integr Bioinform - A hierarchical approach to protein fold prediction. ( 0,659315734406848 )
J. Comput. Biol. - Efficient traversal of beta-sheet protein folding pathways using ensemble models. ( 0,655523818843074 )
J Chem Inf Model - Protein structural statistics with PSS. ( 0,653673163418291 )
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. ( 0,653646251610697 )
J Chem Inf Model - Dihedral-based segment identification and classification of biopolymers II: polynucleotides. ( 0,652787593557716 )
Curr Protoc Bioinformatics - Comparative Protein Structure Modeling Using MODELLER. ( 0,652617447731203 )
Comput. Biol. Med. - Intron identification approaches based on weighted features and fuzzy decision trees. ( 0,650551567998703 )
J Chem Inf Model - Protein secondary structure classification revisited: processing DSSP information with PSSC. ( 0,649911218353202 )
J. Comput. Biol. - Combinatorics of -structures. ( 0,649610105195966 )
Brief. Bioinformatics - Comparative analysis of methods for genome-wide nucleosome cartography. ( 0,648140872531405 )
J Biomed Inform - A similarity network approach for the analysis and comparison of protein sequence/structure sets. ( 0,648029226585619 )
Comput Math Methods Med - DV-curve representation of protein sequences and its application. ( 0,646346315601571 )
Comput Methods Programs Biomed - Pinda: a web service for detection and analysis of intraspecies gene duplication events. ( 0,646314756589655 )
Brief. Bioinformatics - Base-calling for next-generation sequencing platforms. ( 0,644927536231884 )
Comput Methods Programs Biomed - Protein secondary structure prediction using modular reciprocal bidirectional recurrent neural networks. ( 0,641039645456612 )
Comput Biol Chem - Identification and characterization of lysine-methylated sites on histones and non-histone proteins. ( 0,640461401135025 )
J Biomed Inform - A kinetic model-based algorithm to classify NGS short reads by their allele origin. ( 0,636179990466946 )
Brief. Bioinformatics - DNA barcoding: a six-question tour to improve users' awareness about the method. ( 0,636171643911634 )
Sci Data - A repository of assays to quantify 10,000 human proteins by SWATH-MS. ( 0,632455532033676 )
Brief. Bioinformatics - Sequencing technologies and tools for short tandem repeat variation detection. ( 0,629694732891361 )
Brief. Bioinformatics - BamView: visualizing and interpretation of next-generation sequencing read alignments. ( 0,628303005168324 )
Brief. Bioinformatics - Alpha shape and Delaunay triangulation in studies of protein-related interactions. ( 0,625783882011697 )
J Integr Bioinform - Prediction of thioredoxin and glutaredoxin target proteins by identifying reversibly oxidized cysteinyl residues. ( 0,625495584403559 )
J. Comput. Biol. - Statistical significance of threading scores. ( 0,625469889617334 )
Brief. Bioinformatics - A survey of tools for variant analysis of next-generation genome sequencing data. ( 0,624978013914268 )
Sci Data - A draft genome for the African crocodilian trypanosome Trypanosoma grayi. ( 0,624833742354597 )
Brief. Bioinformatics - Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. ( 0,624463042363071 )
J Integr Bioinform - Complementarity of network and sequence information in homologous proteins. ( 0,622403525715288 )
J. Comput. Biol. - Optimization of profile-to-profile alignment parameters for one-dimensional threading. ( 0,621399231572933 )
J Chem Inf Model - Proteins as sponges: a statistical journey along protein structure organization principles. ( 0,6213697660012 )
J. Comput. Biol. - Using structural and evolutionary information to detect and correct pyrosequencing errors in noncoding RNAs. ( 0,621244188772196 )
Comput Biol Chem - Large replication skew domains delimit GC-poor gene deserts in human. ( 0,619372661598922 )
Comput. Biol. Med. - Signal peptide discrimination and cleavage site identification using SVM and NN. ( 0,61918724521786 )
Comput Biol Chem - A local average connectivity-based method for identifying essential proteins from the network level. ( 0,619067794596128 )
J Integr Bioinform - Exceptional single strand DNA word symmetry: analysis of evolutionary potentialities. ( 0,61850342060477 )
Brief. Bioinformatics - Reference databases for taxonomic assignment in metagenomics. ( 0,616951487329421 )
Int J Health Geogr - Linking GPS and travel diary data using sequence alignment in a study of children's independent mobility. ( 0,616412129089517 )
Comput Biol Chem - Circular code motifs in the ribosome decoding center. ( 0,616293223804998 )
J. Comput. Biol. - AREM: aligning short reads from ChIP-sequencing by expectation maximization. ( 0,616184790024626 )
Comput Math Methods Med - Na?ve Bayes classifier with feature selection to identify phage virion proteins. ( 0,615247028084398 )
Comput Biol Chem - A novel empirical mutual information approach to identify co-evolving amino acid positions of influenza A viruses. ( 0,614905602116648 )
J. Comput. Biol. - Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. ( 0,614179906742474 )
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. ( 0,613667510437682 )
Med Biol Eng Comput - Enhanced spatio-temporal alignment of plantar pressure image sequences using B-splines. ( 0,611643334502477 )
J Chem Inf Model - Kink characterization and modeling in transmembrane protein structures. ( 0,61028535363319 )
Comput Biol Chem - Support vector machine with a Pearson VII function kernel for discriminating halophilic and non-halophilic proteins. ( 0,608876784643976 )
J. Comput. Biol. - Tracing the most parsimonious indel history. ( 0,608699149449972 )