REMiner-II: A tool for rapid identification and configuration of repetitive element arrays from large mammalian chromosomes as a single query

Genomics

Volumn 100, Issue 3, 2012, Pages 131-140

  Kim, Woo Chan ^a   Lee, Kang Hoon ^b   Shin, Kyung Seop ^a   You, Ri Na ^a   Lee, Young Kwan ^b   Cho, Kiho ^b   Cho, Dong Ho ^a  

^a Korea Advanced Institute of Science and Technology (KAIST)   (South Korea)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Chromosome wide; Mammalian genome; Mining; RE array; REMiner II; Repetitive element

Indexed keywords

ACCURACY; ALGORITHM; ARTICLE; CHROMOSOME IDENTIFICATION; COMPUTER INTERFACE; CONTROLLED STUDY; DATA ANALYSIS SOFTWARE; DATA EXTRACTION; DATA MINING; GENE LIBRARY; PREDICTION; PRIORITY JOURNAL; PROCESS DEVELOPMENT; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY;

ALGORITHMS; ANIMALS; CHROMOSOMES; COMPUTATIONAL BIOLOGY; DATA MINING; DATABASES, GENETIC; GENOME, HUMAN; HUMANS; INTERNET; MAMMALS; MICE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REPETITIVE SEQUENCES, NUCLEIC ACID; SEQUENCE ALIGNMENT; SOFTWARE; SPECIES SPECIFICITY; TIME FACTORS;

MAMMALIA;

EID: 84865348559     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2012.06.006     Document Type: Article

References (29)

1. Bernal A., Ear U., Kyrpides N. Genomes OnLine Database (GOLD): a monitor of genome projects world-wide. Nucleic Acids Res. 2001, 29:126-127.
2. Lander E.S., Linton L.M., Birren B., Nusbaum C., Zody M.C., Baldwin J., Devon K., Dewar K., Doyle M., FitzHugh W., Funke R., Gage D., Harris K., Heaford A., Howland J., Kann L., Lehoczky J., LeVine R., McEwan P., McKernan K., Meldrim J., Mesirov J.P., Miranda C., Morris W., Naylor J., Raymond C., Rosetti M., Santos R., Sheridan A., Sougnez C., Stange-Thomann N., Stojanovic N., Subramanian A., Wyman D., Rogers J., Sulston J., Ainscough R., Beck S., Bentley D., Burton J., Clee C., Carter N., Coulson A., Deadman R., Deloukas P., Dunham A., Dunham I., Durbin R., French L., Grafham D., Gregory S., Hubbard T., Humphray S., Hunt A., Jones M., Lloyd C., McMurray A., Matthews L., Mercer S., Milne S., Mullikin J.C., Mungall A., Plumb R., Ross M., Shownkeen R., Sims S., Waterston R.H., Wilson R.K., Hillier L.W., McPherson J.D., Marra M.A., Mardis E.R., Fulton L.A., Chinwalla A.T., Pepin K.H., Gish W.R., Chissoe S.L., Wendl M.C., Delehaunty K.D., Miner T.L., Delehaunty A., Kramer J.B., Cook L.L., Fulton R.S., Johnson D.L., Minx P.J., Clifton S.W., Hawkins T., Branscomb E., Predki P., Richardson P., Wenning S., Slezak T., Doggett N., Cheng J.F., Olsen A., Lucas S., Elkin C., Uberbacher E., Frazier M., Gibbs R.A., Muzny D.M., Scherer S.E., Bouck J.B., Sodergren E.J., Worley K.C., Rives C.M., Gorrell J.H., Metzker M.L., Naylor S.L., Kucherlapati R.S., Nelson D.L., Weinstock G.M., Sakaki Y., Fujiyama A., Hattori M., Yada T., Toyoda A., Itoh T., Kawagoe C., Watanabe H., Totoki Y., Taylor T., Weissenbach J., Heilig R., Saurin W., Artiguenave F., Brottier P., Bruls T., Pelletier E., Robert C., Wincker P., Smith D.R., Doucette-Stamm L., Rubenfield M., Weinstock K., Lee H.M., Dubois J., Rosenthal A., Platzer M., Nyakatura G., Taudien S., Rump A., Yang H., Yu J., Wang J., Huang G., Gu J., Hood L., Rowen L., Madan A., Qin S., Davis R.W., Federspiel N.A., Abola A.P., Proctor M.J., Myers R.M., Schmutz J., Dickson M., Grimwood J., Cox D.R., Olson M.V., Kaul R., Shimizu N., Kawasaki K., Minoshima S., Evans G.A., Athanasiou M., Schultz R., Roe B.A., Chen F., Pan H., Ramser J., Lehrach H., Reinhardt R., McCombie W.R., de la Bastide M., Dedhia N., Blocker H., Hornischer K., Nordsiek G., Agarwala R., Aravind L., Bailey J.A., Bateman A., Batzoglou S., Birney E., Bork P., Brown D.G., Burge C.B., Cerutti L., Chen H.C., Church D., Clamp M., Copley R.R., Doerks T., Eddy S.R., Eichler E.E., Furey T.S., Galagan J., Gilbert J.G., Harmon C., Hayashizaki Y., Haussler D., Hermjakob H., Hokamp K., Jang W., Johnson L.S., Jones T.A., Kasif S., Kaspryzk A., Kennedy S., Kent W.J., Kitts P., Koonin E.V., Korf I., Kulp D., Lancet D., Lowe T.M., McLysaght A., Mikkelsen T., Moran J.V., Mulder N., Pollara V.J., Ponting C.P., Schuler G., Schultz J., Slater G., Smit A.F., Stupka E., Szustakowski J., Thierry-Mieg D., Thierry-Mieg J., Wagner L., Wallis J., Wheeler R., Williams A., Wolf Y.I., Wolfe K.H., Yang S.P., Yeh R.F., Collins F., Guyer M.S., Peterson J., Felsenfeld A., Wetterstrand K.A., Patrinos A., Morgan M.J., de Jong P., Catanese J.J., Osoegawa K., Shizuya H., Choi S., Chen Y.J. Initial sequencing and analysis of the human genome. Nature 2001, 409:860-921.
3. Schuler G.D., Boguski M.S., Stewart E.A., Stein L.D., Gyapay G., Rice K., White R.E., Rodriguez-Tome P., Aggarwal A., Bajorek E., Bentolila S., Birren B.B., Butler A., Castle A.B., Chiannilkulchai N., Chu A., Clee C., Cowles S., Day P.J., Dibling T., Drouot N., Dunham I., Duprat S., East C., Edwards C., Fan J.B., Fang N., Fizames C., Garrett C., Green L., Hadley D., Harris M., Harrison P., Brady S., Hicks A., Holloway E., Hui L., Hussain S., Louis-Dit-Sully C., Ma J., MacGilvery A., Mader C., Maratukulam A., Matise T.C., McKusick K.B., Morissette J., Mungall A., Muselet D., Nusbaum H.C., Page D.C., Peck A., Perkins S., Piercy M., Qin F., Quackenbush J., Ranby S., Reif T., Rozen S., Sanders C., She X., Silva J., Slonim D.K., Soderlund C., Sun W.L., Tabar P., Thangarajah T., Vega-Czarny N., Vollrath D., Voyticky S., Wilmer T., Wu X., Adams M.D., Auffray C., Walter N.A., Brandon R., Dehejia A., Goodfellow P.N., Houlgatte R., Hudson J.R., Ide S.E., Iorio K.R., Lee W.Y., Seki N., Nagase T., Ishikawa K., Nomura N., Phillips C., Polymeropoulos M.H., Sandusky M., Schmitt K., Berry R., Swanson K., Torres R., Venter J.C., Sikela J.M., Beckmann J.S., Weissenbach J., Myers R.M., Cox D.R., James M.R., Bentley D., Deloukas P., Lander E.S., Hudson T.J. A gene map of the human genome. Science 1996, 274:540-546.
4. Venter J.C., Adams M.D., Myers E.W., Li P.W., Mural R.J., Sutton G.G., Smith H.O., Yandell M., Evans C.A., Holt R.A., Gocayne J.D., Amanatides P., Ballew R.M., Huson D.H., Wortman J.R., Zhang Q., Kodira C.D., Zheng X.H., Chen L., Skupski M., Subramanian G., Thomas P.D., Zhang J., Gabor Miklos G.L., Nelson C., Broder S., Clark A.G., Nadeau J., McKusick V.A., Zinder N., Levine A.J., Roberts R.J., Simon M., Slayman C., Hunkapiller M., Bolanos R., Delcher A., Dew I., Fasulo D., Flanigan M., Florea L., Halpern A., Hannenhalli S., Kravitz S., Levy S., Mobarry C., Reinert K., Remington K., Abu-Threideh J., Beasley E., Biddick K., Bonazzi V., Brandon R., Cargill M., Chandramouliswaran I., Charlab R., Chaturvedi K., Deng Z., Di Francesco V., Dunn P., Eilbeck K., Evangelista C., Gabrielian A.E., Gan W., Ge W., Gong F., Gu Z., Guan P., Heiman T.J., Higgins M.E., Ji R.R., Ke Z., Ketchum K.A., Lai Z., Lei Y., Li Z., Li J., Liang Y., Lin X., Lu F., Merkulov G.V., Milshina N., Moore H.M., Naik A.K., Narayan V.A., Neelam B., Nusskern D., Rusch D.B., Salzberg S., Shao W., Shue B., Sun J., Wang Z., Wang A., Wang X., Wang J., Wei M., Wides R., Xiao C., Yan C., Yao A., Ye J., Zhan M., Zhang W., Zhang H., Zhao Q., Zheng L., Zhong F., Zhong W., Zhu S., Zhao S., Gilbert D., Baumhueter S., Spier G., Carter C., Cravchik A., Woodage T., Ali F., An H., Awe A., Baldwin D., Baden H., Barnstead M., Barrow I., Beeson K., Busam D., Carver A., Center A., Cheng M.L., Curry L., Danaher S., Davenport L., Desilets R., Dietz S., Dodson K., Doup L., Ferriera S., Garg N., Gluecksmann A., Hart B., Haynes J., Haynes C., Heiner C., Hladun S., Hostin D., Houck J., Howland T., Ibegwam C., Johnson J., Kalush F., Kline L., Koduru S., Love A., Mann F., May D., McCawley S., McIntosh T., McMullen I., Moy M., Moy L., Murphy B., Nelson K., Pfannkoch C., Pratts E., Puri V., Qureshi H., Reardon M., Rodriguez R., Rogers Y.H., Romblad D., Ruhfel B., Scott R., Sitter C., Smallwood M., Stewart E., Strong R., Suh E., Thomas R., Tint N.N., Tse S., Vech C., Wang G., Wetter J., Williams S., Williams M., Windsor S., Winn-Deen E., Wolfe K., Zaveri J., Zaveri K., Abril J.F., Guigo R., Campbell M.J., Sjolander K.V., Karlak B., Kejariwal A., Mi H., Lazareva B., Hatton T., Narechania A., Diemer K., Muruganujan A., Guo N., Sato S., Bafna V., Istrail S., Lippert R., Schwartz R., Walenz B., Yooseph S., Allen D., Basu A., Baxendale J., Blick L., Caminha M., Carnes-Stine J., Caulk P., Chiang Y.H., Coyne M., Dahlke C., Mays A., Dombroski M., Donnelly M., Ely D., Esparham S., Fosler C., Gire H., Glanowski S., Glasser K., Glodek A., Gorokhov M., Graham K., Gropman B., Harris M., Heil J., Henderson S., Hoover J., Jennings D., Jordan C., Jordan J., Kasha J., Kagan L., Kraft C., Levitsky A., Lewis M., Liu X., Lopez J., Ma D., Majoros W., McDaniel J., Murphy S., Newman M., Nguyen T., Nguyen N., Nodell M., Pan S., Peck J., Peterson M., Rowe W., Sanders R., Scott J., Simpson M., Smith T., Sprague A., Stockwell T., Turner R., Venter E., Wang M., Wen M., Wu D., Wu M., Xia A., Zandieh A., Zhu X. The sequence of the human genome. Science 2001, 291:1304-1351.
5. Waterston R.H., Lindblad-Toh K., Birney E., Rogers J., Abril J.F., Agarwal P., Agarwala R., Ainscough R., Alexandersson M., An P., Antonarakis S.E., Attwood J., Baertsch R., Bailey J., Barlow K., Beck S., Berry E., Birren B., Bloom T., Bork P., Botcherby M., Bray N., Brent M.R., Brown D.G., Brown S.D., Bult C., Burton J., Butler J., Campbell R.D., Carninci P., Cawley S., Chiaromonte F., Chinwalla A.T., Church D.M., Clamp M., Clee C., Collins F.S., Cook L.L., Copley R.R., Coulson A., Couronne O., Cuff J., Curwen V., Cutts T., Daly M., David R., Davies J., Delehaunty K.D., Deri J., Dermitzakis E.T., Dewey C., Dickens N.J., Diekhans M., Dodge S., Dubchak I., Dunn D.M., Eddy S.R., Elnitski L., Emes R.D., Eswara P., Eyras E., Felsenfeld A., Fewell G.A., Flicek P., Foley K., Frankel W.N., Fulton L.A., Fulton R.S., Furey T.S., Gage D., Gibbs R.A., Glusman G., Gnerre S., Goldman N., Goodstadt L., Grafham D., Graves T.A., Green E.D., Gregory S., Guigo R., Guyer M., Hardison R.C., Haussler D., Hayashizaki Y., Hillier L.W., Hinrichs A., Hlavina W., Holzer T., Hsu F., Hua A., Hubbard T., Hunt A., Jackson I., Jaffe D.B., Johnson L.S., Jones M., Jones T.A., Joy A., Kamal M., Karlsson E.K., Karolchik D., Kasprzyk A., Kawai J., Keibler E., Kells C., Kent W.J., Kirby A., Kolbe D.L., Korf I., Kucherlapati R.S., Kulbokas E.J., Kulp D., Landers T., Leger J.P., Leonard S., Letunic I., Levine R., Li J., Li M., Lloyd C., Lucas S., Ma B., Maglott D.R., Mardis E.R., Matthews L., Mauceli E., Mayer J.H., McCarthy M., McCombie W.R., McLaren S., McLay K., McPherson J.D., Meldrim J., Meredith B., Mesirov J.P., Miller W., Miner T.L., Mongin E., Montgomery K.T., Morgan M., Mott R., Mullikin J.C., Muzny D.M., Nash W.E., Nelson J.O., Nhan M.N., Nicol R., Ning Z., Nusbaum C., O'Connor M.J., Okazaki Y., Oliver K., Overton-Larty E., Pachter L., Parra G., Pepin K.H., Peterson J., Pevzner P., Plumb R., Pohl C.S., Poliakov A., Ponce T.C., Ponting C.P., Potter S., Quail M., Reymond A., Roe B.A., Roskin K.M., Rubin E.M., Rust A.G., Santos R., Sapojnikov V., Schultz B., Schultz J., Schwartz M.S., Schwartz S., Scott C., Seaman S., Searle S., Sharpe T., Sheridan A., Shownkeen R., Sims S., Singer J.B., Slater G., Smit A., Smith D.R., Spencer B., Stabenau A., Stange-Thomann N., Sugnet C., Suyama M., Tesler G., Thompson J., Torrents D., Trevaskis E., Tromp J., Ucla C., Ureta-Vidal A., Vinson J.P., Von Niederhausern A.C., Wade C.M., Wall M., Weber R.J., Weiss R.B., Wendl M.C., West A.P., Wetterstrand K., Wheeler R., Whelan S., Wierzbowski J., Willey D., Williams S., Wilson R.K., Winter E., Worley K.C., Wyman D., Yang S., Yang S.P., Zdobnov E.M., Zody M.C., Lander E.S. Initial sequencing and comparative analysis of the mouse genome. Nature 2002, 420:520-562.
6. Deininger P.L., Batzer M.A. Mammalian retroelements. Genome Res. 2002, 12:1455-1465.
7. Dion V., Wilson J.H. Instability and chromatin structure of expanded trinucleotide repeats. Trends Genet. 2009, 25:288-297.
8. Fondon J.W., Garner H.R. Molecular origins of rapid and continuous morphological evolution. Proc. Natl. Acad. Sci. U. S. A. 2004, 101:18058-18063.
9. Lee K.H., Lee Y.K., Kwon D.N., Chiu S., Chew V., Rah H., Kujawski G., Melhem R., Hsu K., Chung C., Greenhalgh D.G., Cho K. Identification of a unique library of complex, but ordered, arrays of repetitive elements in the human genome and implication of their potential involvement in pathobiology. Exp. Mol. Pathol. 2011, 90:300-311.
10. Chung B.I., Lee K.H., Shin K.S., Kim W.C., Kwon D.N., You R.N., Lee Y.K., Cho K., Cho D.H. REMiner: a tool for unbiased mining and analysis of repetitive elements and their arrangement structures of large chromosomes. Genomics 2011, 98:381-389.
11. Bedell J.A., Korf I., Gish W. MaskerAid: a performance enhancement to RepeatMasker. Bioinformatics 2000, 16:1040-1041.
12. Li X., Kahveci T., Settles A.M. A novel genome-scale repeat finder geared towards transposons. Bioinformatics 2008, 24:468-476.
13. Ma B., Tromp J., Li M. PatternHunter: faster and more sensitive homology search. Bioinformatics 2002, 18:440-445.
14. Tatusova T.A., Madden T.L. BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol. Lett. 1999, 174:247-250.
15. Jurka J., Klonowski P., Dagman V., Pelton P. CENSOR-a program for identification and elimination of repetitive elements from DNA sequences. Comput. Chem. 1996, 20:119-121.
16. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 1990, 215:403-410.
17. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25:3389-3402.
18. Lerat E. Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs. Heredity 2010, 104:520-533.
19. Achaz G., Boyer F., Rocha E.P., Viari A., Coissac E. Repseek, a tool to retrieve approximate repeats from large DNA sequences. Bioinformatics 2007, 23:119-121.
20. Chen Y., Zhou F., Li G., Xu Y. MUST: a system for identification of miniature inverted-repeat transposable elements and applications to Anabaena variabilis and Haloquadratum walsbyi. Gene 2009, 436:1-7.
21. Edgar R.C., Myers E.W. PILER: identification and classification of genomic repeats. Bioinformatics 2005, 21(Suppl. 1):i152-i158.
22. Ellinghaus D., Kurtz S., Willhoeft U. LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinforma. 2008, 9:18.
23. Morgulis A., Gertz E.M., Schaffer A.A., Agarwala R. A fast and symmetric DUST implementation to mask low-complexity DNA sequences. J. Comput. Biol. 2006, 13:1028-1040.
24. Watson J.D., Crick F.H. Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid. Nature 1953, 171:737-738.
25. Jacob A., Lancaster J., Buhler J., Chamberlain R.D. FPGA-accelerated seed generation in Mercury BLASTP. IEEE FCCM 2007, 95-106.
26. Kasap S., Benkrid K., Liu Y. Design and implementation of an FPGA-based core for gapped BLAST sequence alignment with the two-hit method. Eng. Lett. 2008, 16:443-452.
27. Zhang Z., Schwartz S., Wagner L., Miller W. A greedy algorithm for aligning DNA sequences. J. Comput. Biol. 2000, 7:203-214.
28. Smit A., Hubley R., Green P. RepeatMasker Open-3.0 1996-2010, .
29. Xu Z., Wang H. LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res. 2007, 35:W265-W268.