J. Comput. Biol. - PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences.

Tópicos

{ assess(1506) score(1403) qualiti(1306) }
{ high(1669) rate(1365) level(1280) }
{ algorithm(1844) comput(1787) effici(935) }
{ model(2341) predict(2261) use(1141) }
{ sampl(1606) size(1419) use(1276) }
{ sequenc(1873) structur(1644) protein(1328) }
{ imag(2830) propos(1344) filter(1198) }
{ error(1145) method(1030) estim(1020) }
{ general(901) number(790) one(736) }
{ method(984) reconstruct(947) comput(926) }
{ spatial(1525) area(1432) region(1030) }
{ model(2656) set(1616) predict(1553) }
{ structur(1116) can(940) graph(676) }
{ drug(1928) target(777) effect(648) }
{ method(2212) result(1239) propos(1039) }
{ model(3404) distribut(989) bayesian(671) }
{ take(945) account(800) differ(722) }
{ learn(2355) train(1041) set(1003) }
{ data(1714) softwar(1251) tool(1186) }
{ case(1353) use(1143) diagnosi(1136) }
{ howev(809) still(633) remain(590) }
{ risk(3053) factor(974) diseas(938) }
{ cancer(2502) breast(956) screen(824) }
{ estim(2440) model(1874) function(577) }
{ decis(3086) make(1611) patient(1517) }
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{ system(1976) rule(880) can(841) }
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{ bind(1733) structur(1185) ligand(1036) }
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{ network(2748) neural(1063) input(814) }
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{ extract(1171) text(1153) clinic(932) }
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{ control(1307) perform(991) simul(935) }
{ model(2220) cell(1177) simul(1124) }
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{ compound(1573) activ(1297) structur(1058) }
{ perform(1367) use(1326) method(1137) }
{ studi(1119) effect(1106) posit(819) }
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{ 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) }
{ state(1844) use(1261) util(961) }
{ 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) }
{ cost(1906) reduc(1198) effect(832) }
{ group(2977) signific(1463) compar(1072) }
{ 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) }
{ health(1844) social(1437) communiti(874) }
{ use(976) code(926) identifi(902) }
{ use(1733) differ(960) four(931) }
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{ implement(1333) system(1263) develop(1122) }
{ survey(1388) particip(1329) question(1065) }
{ 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

We introduce PASTA, a new multiple sequence alignment algorithm. PASTA uses a new technique to produce an alignment given a guide tree that enables it to be both highly scalable and very accurate. We present a study on biological and simulated data with up to 200,000 sequences, showing that PASTA produces highly accurate alignments, improving on the accuracy and scalability of the leading alignment methods (including SAT?). We also show that trees estimated on PASTA alignments are highly accurate--slightly better than SAT? trees, but with substantial improvements relative to other methods. Finally, PASTA is faster than SAT?, highly parallelizable, and requires relatively little memory.

Resumo Limpo

introduc pasta new multipl sequenc align algorithm pasta use new techniqu produc align given guid tree enabl high scalabl accur present studi biolog simul data sequenc show pasta produc high accur align improv accuraci scalabl lead align method includ sat also show tree estim pasta align high accurateslight better sat tree substanti improv relat method final pasta faster sat high paralleliz requir relat littl memori

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