Versatile and open software for comparing large genomes
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* Corresponding author: Steven L Salzberg salzberg@tigr.org
Genome Biology 2004, 5:R12 doi:10.1186/gb-2004-5-2-r12
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BioMed Central: 90 citations
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Short Report
Jingwei Jiang, Jun Li, Hoi Shan Kwan, Chun Hang Au, Patrick Tik Wan Law, Lei Li, Kai Man Kam, Julia Mei Lun Ling, Frederick C Leung BMC Research Notes 2012, 5:80 (31 January 2012) |
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Research article
Anding Zhang, Ming Yang, Pan Hu, Jiayan Wu, Bo Chen, Yafeng Hua, Jun Yu, Huanchun Chen, Jingfa Xiao, Meilin Jin BMC Genomics 2011, 12:523 (25 October 2011) |
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Research article
Matthew G Links, Eric Holub, Rays HY Jiang, Andrew G Sharpe, Dwayne Hegedus, Elena Beynon, Dean Sillito, Wayne E Clarke, Shihomi Uzuhashi, Mohammad H Borhan BMC Genomics 2011, 12:503 (13 October 2011) |
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Research article
Queenie WT Chan, R Scott Cornman, Inanc Birol, Nancy Y Liao, Simon K Chan, T Roderick Docking, Shaun D Jackman, Greg A Taylor, Steven JM Jones, Dirk C de Graaf, Jay D Evans, Leonard J Foster BMC Genomics 2011, 12:450 (16 September 2011) |
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Software review
SNIT: SNP identification for strain typing Ravi Vijaya Satya, Nela Zavaljevski, Jaques Reifman Source Code for Biology and Medicine 2011, 6:14 (8 September 2011) |
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Proceedings
Brian M Forde, B Neville, Michelle M O’ Donnell, E Riboulet-Bisson, M J Claesson, Avril Coghlan, R Ross, Paul W O’ Toole Microbial Cell Factories 2011, 10(Suppl 1):S13 (30 August 2011) |
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Research article
Henk C den Bakker, Andrea I Moreno Switt, Gregory Govoni, Craig A Cummings, Matthew L Ranieri, Lovorka Degoricija, Karin Hoelzer, Lorraine D Rodriguez-Rivera, Stephanie Brown, Elena Bolchacova, Manohar R Furtado, Martin Wiedmann BMC Genomics 2011, 12:425 (22 August 2011) |
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Software
BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons Nabil-Fareed Alikhan, Nicola K Petty, Nouri L Ben Zakour, Scott A Beatson BMC Genomics 2011, 12:402 (8 August 2011) The BLAST Ring Image Generator (BRIG) software allows users to rapidly visualize comparisons between large numbers of bacterial genomes, including unfinished or unassembled genome data, in a single image.
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Research article
Therese Håfström, Désirée S Jansson , Bo Segerman BMC Genomics 2011, 12:395 (4 August 2011) |
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Research article
Frank A Feltus, Christopher A Saski, Keithanne Mockaitis, Niina Haiminen, Laxmi Parida, Zachary Smith, James Ford, Margaret E Staton, Stephen P Ficklin, Barbara P Blackmon, Chun-Huai Cheng, Raymond J Schnell, David N Kuhn, Juan-Carlos Motamayor BMC Genomics 2011, 12:379 (27 July 2011) |
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Research
Molecular characterization of the uncultivatable hemotropic bacterium Mycoplasma haemofelis Emily N Barker, Alistair C Darby, Chris R Helps, Iain R Peters, Kate J Heesom, Christopher J Arthur, Ben Crossett, Margaret A Hughes, Alan D Radford, Séverine Tasker Veterinary Research 2011, 42:83 (12 July 2011) |
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Research article
Melissa ML Wong, Charles H Cannon, Ratnam Wickneswari BMC Genomics 2011, 12:342 (5 July 2011) |
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Software review
CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes Marco Galardini, Emanuele G Biondi, Marco Bazzicalupo, Alessio Mengoni Source Code for Biology and Medicine 2011, 6:11 (21 June 2011) |
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Methodology article
Querying large read collections in main memory: a versatile data structure Nicolas Philippe, Mikaël Salson, Thierry Lecroq, Martine Léonard, Thérèse Commes, Eric Rivals BMC Bioinformatics 2011, 12:242 (17 June 2011) |
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Research article
Phylogeography of Francisella tularensis subspecies holarctica from the country of Georgia Gvantsa Chanturia, Dawn N Birdsell, Merab Kekelidze, Ekaterine Zhgenti, George Babuadze, Nikoloz Tsertsvadze, Shota Tsanava, Paata Imnadze, Stephen M Beckstrom-Sternberg, James S Beckstrom-Sternberg, Mia D Champion, Shripad Sinari, Miklos Gyuranecz, Jason Farlow, Amanda H Pettus, Emily L Kaufman, Joseph D Busch, Talima Pearson, Jeffrey T Foster, Amy J Vogler, David M Wagner, Paul Keim BMC Microbiology 2011, 11:139 (17 June 2011) |
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Research
Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths Jacob Enk, Alison Devault, Regis Debruyne, Christine E King, Todd Treangen, Dennis O'Rourke, Steven L Salzberg, Daniel Fisher, Ross MacPhee, Hendrik Poinar Genome Biology 2011, 12:R51 (31 May 2011) A surprising mtDNA phylogeny suggests that North American woolly mammoths bred with the distinct Columbian mammoth species
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Research
A novel mode of chromosomal evolution peculiar to filamentous Ascomycete fungi James K Hane, Thierry Rouxel, Barbara J Howlett, Gert HJ Kema, Stephen B Goodwin, Richard P Oliver Genome Biology 2011, 12:R45 (24 May 2011) Mesosynteny, in which genes are maintained on the same chromosome but in different orders, is revealed in different ascomycete species
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Research
Linkage disequilibrium based genotype calling from low-coverage shotgun sequencing reads Jorge Duitama, Justin Kennedy, Sanjiv Dinakar, Yözen Hernández, Yufeng Wu, Ion I Măndoiu BMC Bioinformatics 2011, 12(Suppl 1):S53 (15 February 2011) |
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Methodology article
A genome alignment algorithm based on compression Minh Cao, Trevor I Dix, Lloyd Allison BMC Bioinformatics 2010, 11:599 (16 December 2010) |
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Research article
An algorithm for automated closure during assembly Sergey Koren, Jason R Miller, Brian P Walenz, Granger Sutton BMC Bioinformatics 2010, 11:457 (10 September 2010) |
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Research
Bernice Meng Qi Sim, Narisara Chantratita, Wen Fong Ooi, Tannistha Nandi, Ryan Tewhey, Vanaporn Wuthiekanun, Janjira Thaipadungpanit, Sarinna Tumapa, Pramila Ariyaratne, Wing-Kin Sung, Xiao Hui Sem, Hui Hoon Chua, Kalpana Ramnarayanan, Chi Ho Lin, Yichun Liu, Edward J Feil, Mindy B Glass, Gladys Tan, Sharon J Peacock, Patrick Tan Genome Biology 2010, 11:R89 (27 August 2010) Sequencing and microarray analyses of non-pathogenic and pathogenic Burkholderia isolates reveals insight into the factors underlying the acquisition of pathogenesis.
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Research article
Jörg Barke, Ryan F Seipke, Sabine Grüschow, Darren Heavens, Nizar Drou, Mervyn J Bibb, Rebecca JM Goss, Douglas W Yu, Matthew I Hutchings BMC Biology 2010, 8:109 (26 August 2010) Leaf-cutter ants cultivate fungi for food, and provide antifungals from associated bacteria to weed out unwanted necrotizing species. Controversy over whether the bacteria are vertically transmitted symbionts or horizontally transmitted environmental species is now resolved: they’re both.
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Research article
Eugeni Belda, Andrés Moya, Stephen Bentley, Francisco J Silva BMC Genomics 2010, 11:449 (22 July 2010) |
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Software
A high-throughput pipeline for the design of real-time PCR signatures Ravi Vijaya Satya, Kamal Kumar, Nela Zavaljevski, Jaques Reifman BMC Bioinformatics 2010, 11:340 (23 June 2010) |
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Research article
Michael D Harwich, Joao M Alves, Gregory A Buck, Jerome F Strauss, Jennifer L Patterson, Aminat T Oki, Philippe H Girerd, Kimberly K Jefferson BMC Genomics 2010, 11:375 (11 June 2010) |
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Research article
Max Farnbacher, Thomas Jahns, Dirk Willrodt, Rolf Daniel, Rainer Haas, Alexander Goesmann, Stefan Kurtz, Gabriele Rieder BMC Genomics 2010, 11:335 (27 May 2010) |
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Research article
Bradd J Haley, Christopher J Grim, Nur A Hasan, Seon-Young Choi, Jongsik Chun, Thomas S Brettin, David C Bruce, Jean F Challacombe, J Chris Detter, Cliff S Han, Anwar Huq, Rita R Colwell BMC Microbiology 2010, 10:154 (27 May 2010) |
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Research article
Cgaln: fast and space-efficient whole-genome alignment Ryuichiro Nakato, Osamu Gotoh BMC Bioinformatics 2010, 11:224 (30 April 2010) |
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Research
Fabrice Touzain, Erick Denamur, Claudine Médigue, Valérie Barbe, Meriem El Karoui, Marie-Agnès Petit Genome Biology 2010, 11:R45 (30 April 2010) Comparison of all available genomes of three bacterial species suggests that a large part of genome diversity is contributed by short regions. |
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Research article
Leandro M Moreira, Nalvo F Almeida, Neha Potnis, Luciano A Digiampietri, Said S Adi, Julio C Bortolossi, Ana C da Silva, Aline M da Silva, Fabrício E de Moraes, Julio C de Oliveira, Robson F de Souza, Agda P Facincani, André L Ferraz, Maria I Ferro, Luiz R Furlan, Daniele F Gimenez, Jeffrey B Jones, Elliot W Kitajima, Marcelo L Laia, Rui P Leite, Milton Y Nishiyama, Julio Rodrigues Neto, Letícia A Nociti, David J Norman, Eric H Ostroski, Haroldo A Pereira, Brian J Staskawicz, Renata I Tezza, Jesus A Ferro, Boris A Vinatzer, João C Setubal et al. BMC Genomics 2010, 11:238 (13 April 2010) |
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Method
Detection and correction of false segmental duplications caused by genome mis-assembly David R Kelley, Steven L Salzberg Genome Biology 2010, 11:R28 (10 March 2010) A method for determining false segmental duplications in vertebrate genomes, thus correcting mis-assemblies and providing more accurate estimates of duplications. |
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Research article
Matthew W Gilmour, Morag Graham, Gary Van Domselaar, Shaun Tyler, Heather Kent, Keri M Trout-Yakel, Oscar Larios, Vanessa Allen, Barbara Lee, Celine Nadon BMC Genomics 2010, 11:120 (18 February 2010) |
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Research
Phylogenetic comparative assembly Peter Husemann, Jens Stoye Algorithms for Molecular Biology 2010, 5:3 (4 January 2010) This article is part of a collection on Selected papers from WABI... |
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Research
Genomic characterization of the Yersinia genus Peter E Chen, Christopher Cook, Andrew C Stewart, Niranjan Nagarajan, Dan D Sommer, Mihai Pop, Brendan Thomason, Maureen Thomason, Shannon Lentz, Nichole Nolan, Shanmuga Sozhamannan, Alexander Sulakvelidze, Alfred Mateczun, Lei Du, Michael E Zwick, Timothy D Read Genome Biology 2010, 11:R1 (4 January 2010) Comparative |
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Proceedings
Jittima Piriyapongsa, Chumpol Ngamphiw, Anunchai Assawamakin, Pongsakorn Wangkumhang, Payiarat Suwannasri, Uttapong Ruangrit, Gallissara Agavatpanitch, Sissades Tongsima BMC Genomics 2009, 10(Suppl 3):S4 (3 December 2009) |
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Research article
Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer Talima Pearson, Philip Giffard, Stephen Beckstrom-Sternberg, Raymond Auerbach, Heidie Hornstra, Apichai Tuanyok, Erin P Price, Mindy B Glass, Benjamin Leadem, James S Beckstrom-Sternberg, Gerard J Allan, Jeffrey T Foster, David M Wagner, Richard T Okinaka, Siew Sim, Ofori Pearson, Zaining Wu, Jean Chang, Rajinder Kaul, Alex R Hoffmaster, Thomas S Brettin, Richard A Robison, Mark Mayo, Jay E Gee, Patrick Tan, Bart J Currie, Paul Keim BMC Biology 2009, 7:78 (18 November 2009) Despite a high level of lateral gene transfer, the phylogeny of Burkholderia pseudomallei is resolved by SNPs in orthologous shared regions, enabling a wider gene-based analysis to define two populations, ancestral Australian, and South East Asian, separated by the Wallace Line.
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Research article
Ji Qi, Asela J Wijeratne, Lynn P Tomsho, Yi Hu, Stephan C Schuster, Hong Ma BMC Genomics 2009, 10:475 (15 October 2009) |
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Research article
Karen K Hill, Gary Xie, Brian T Foley, Theresa J Smith, Amy C Munk, David Bruce, Leonard A Smith, Thomas S Brettin, John C Detter BMC Biology 2009, 7:66 (5 October 2009) Botulinum neurotoxin genes in Clostridium strains are found associated with insertion elements and recombinases, and show evidence of many recombination events, supporting the importance of horizontal gene transfer and recombination in pathogen evolution.
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Research article
David J Studholme, Selena Ibanez, Daniel MacLean, Jeffery L Dangl, Jeff H Chang, John P Rathjen BMC Genomics 2009, 10:395 (24 August 2009) |
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Research article
Fumito Maruyama, Mitsuhiko Kobata, Ken Kurokawa, Keishin Nishida, Atsuo Sakurai, Kazuhiko Nakano, Ryota Nomura, Shigetada Kawabata, Takashi Ooshima, Kenta Nakai, Masahira Hattori, Shigeyuki Hamada, Ichiro Nakagawa BMC Genomics 2009, 10:358 (5 August 2009) |
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Research article
Brucella microti: the genome sequence of an emerging pathogen Stéphane Audic, Magali Lescot, Jean-Michel Claverie, Holger C Scholz BMC Genomics 2009, 10:352 (4 August 2009) |
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Methodology article
A compartmentalized approach to the assembly of physical maps Serdar Bozdag, Timothy J Close, Stefano Lonardi BMC Bioinformatics 2009, 10:217 (15 July 2009) |
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Research
A whole-genome assembly of the domestic cow, Bos taurus Aleksey V Zimin, Arthur L Delcher, Liliana Florea, David R Kelley, Michael C Schatz, Daniela Puiu, Finnian Hanrahan, Geo Pertea, Curtis P Van Tassell, Tad S Sonstegard, Guillaume Marçais, Michael Roberts, Poorani Subramanian, James A Yorke, Steven L Salzberg Genome Biology 2009, 10:R42 (24 April 2009) A cow whole-genome assembly of 2.86 billion base pairs that closes gaps and corrects previously-described inversions and deletions as well as describing a portion of the Y chromosome.
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Methodology article
Donna M Toleno, Gabriel Renaud, Tyra G Wolfsberg, Munirul Islam, Derek E Wildman, Kimberly D Siegmund, Joseph G Hacia BMC Bioinformatics 2009, 10:77 (5 March 2009) |
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Research
Crystallizing short-read assemblies around seeds Mohammad Hossain, Navid Azimi, Steven Skiena BMC Bioinformatics 2009, 10(Suppl 1):S16 (30 January 2009) |
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Research article
Natalia Volfovsky, Taras K Oleksyk, Kristine C Cruz, Ann L Truelove, Robert M Stephens, Michael W Smith BMC Genomics 2009, 10:51 (26 January 2009) |
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Research
Jean-Marc Rolain, Patrice François, David Hernandez, Fadi Bittar, Hervé Richet, Ghislain Fournous, Yves Mattenberger, Emmanuelle Bosdure, Nathalie Stremler, Jean-Christophe Dubus, Jacques Sarles, Martine Reynaud-Gaubert, Stephanie Boniface, Jacques Schrenzel, Didier Raoult Biology Direct 2009, 4:1 (13 January 2009) |
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Research article
Conservation in the face of diversity: multistrain analysis of an intracellular bacterium Michael J Dark, David R Herndon, Lowell S Kappmeyer, Mikel P Gonzales, Elizabeth Nordeen, Guy H Palmer, Donald P Knowles, Kelly A Brayton BMC Genomics 2009, 10:16 (11 January 2009) |
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Research article
Comparative genomics of vesicomyid clam (Bivalvia: Mollusca) chemosynthetic symbionts Irene LG Newton, Peter R Girguis, Colleen M Cavanaugh BMC Genomics 2008, 9:585 (4 December 2008) |
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Research article
Hao Wang, Zhao Xu, Hongjie Yu BMC Genomics 2008, 9:565 (27 November 2008) |
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Database
Hélène Chiapello, Annie Gendrault, Christophe Caron, Jérome Blum, Marie-Agnès Petit, Meriem El Karoui BMC Bioinformatics 2008, 9:498 (27 November 2008) |
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Methodology article
In silico microarray probe design for diagnosis of multiple pathogens Ravi Vijaya Satya, Nela Zavaljevski, Kamal Kumar, Elizabeth Bode, Susana Padilla, Leonard Wasieloski, Jeanne Geyer, Jaques Reifman BMC Genomics 2008, 9:496 (21 October 2008) |
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Research article
A comparative computational analysis of nonautonomous Helitron elements between maize and rice Michael Sweredoski, Leah DeRose-Wilson, Brandon S Gaut BMC Genomics 2008, 9:467 (8 October 2008) |
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Research article
Michael E Reith, Rama K Singh, Bruce Curtis, Jessica M Boyd, Anne Bouevitch, Jennifer Kimball, Janet Munholland, Colleen Murphy, Darren Sarty, Jason Williams, John HE Nash, Stewart C Johnson, Laura L Brown BMC Genomics 2008, 9:427 (18 September 2008) The genome sequence of the bacterium Aeromonas salmonicida and the comparison of it to Aeromonas hydrophila yields new insights into the evolution and virulence factors that cause furunculusis, a bacterial septicaemia, in salmonid fish.
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Software
GenomeMatcher: A graphical user interface for DNA sequence comparison Yoshiyuki Ohtsubo, Wakako Ikeda-Ohtsubo, Yuji Nagata, Masataka Tsuda BMC Bioinformatics 2008, 9:376 (16 September 2008) |
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Methodology article
ReRep: Computational detection of repetitive sequences in genome survey sequences (GSS) Thomas D Otto, Leonardo HF Gomes, Marcelo Alves-Ferreira, Antonio B de Miranda, Wim M Degrave BMC Bioinformatics 2008, 9:366 (9 September 2008) |
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Research article
Wei Zhu, Shu Ouyang, Marina Iovene, Kimberly O'Brien, Hue Vuong, Jiming Jiang, C Robin Buell BMC Genomics 2008, 9:286 (13 June 2008) |
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Methodology
Jeremy D Edwards, Jaroslav Janda, Megan T Sweeney, Ambika B Gaikwad, Bin Liu, Hei Leung, David W Galbraith Plant Methods 2008, 4:13 (29 May 2008) |
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Research article
Rose Cattolico, Michael A Jacobs, Yang Zhou, Jean Chang, Melinda Duplessis, Terry Lybrand, John McKay, Han Ong, Elizabeth Sims, Gabrielle Rocap BMC Genomics 2008, 9:211 (8 May 2008) |
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Research article
Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A Steven L Salzberg, Daniel D Sommer, Michael C Schatz, Adam M Phillippy, Pablo D Rabinowicz, Seiji Tsuge, Ayako Furutani, Hirokazu Ochiai, Arthur L Delcher, David Kelley, Ramana Madupu, Daniela Puiu, Diana Radune, Martin Shumway, Cole Trapnell, Gudlur Aparna, Gopaljee Jha, Alok Pandey, Prabhu B Patil, Hiromichi Ishihara, Damien F Meyer, Boris Szurek, Valerie Verdier, Ralf Koebnik, J Maxwell Dow, Robert P Ryan, Hisae Hirata, Shinji Tsuyumu, Sang Won Lee, Pamela C Ronald, Ramesh V Sonti, Marie-Anne Van Sluys, Jan E Leach, Frank F White, Adam J Bogdanove et al. BMC Genomics 2008, 9:204 (1 May 2008) |
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Methodology article
A high-throughput pipeline for designing microarray-based pathogen diagnostic assays Ravi Vijaya Satya, Nela Zavaljevski, Kamal Kumar, Jaques Reifman BMC Bioinformatics 2008, 9:185 (10 April 2008) |
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Research
xMAN: extreme MApping of OligoNucleotides Wei Li, Jason S Carroll, Myles Brown, X Shirley Liu BMC Genomics 2008, 9(Suppl 1):S20 (20 March 2008) |
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Method
DNA signatures for detecting genetic engineering in bacteria Jonathan E Allen, Shea N Gardner, Tom R Slezak Genome Biology 2008, 9:R56 (18 March 2008) New computational tools were used to find a robust set of DNA oligomers that can distinguish artificial vector sequences from all available background viral and bacterial genomes. |
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Software
Genome assembly forensics: finding the elusive mis-assembly Adam M Phillippy, Michael C Schatz, Mihai Pop Genome Biology 2008, 9:R55 (14 March 2008) A collection of software tools is combined for the first time in an automated pipeline for detecting large-scale genome assembly errors and for validating genome assemblies. |
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Methodology article
Multiple organism algorithm for finding ultraconserved elements Scott Christley, Neil F Lobo, Greg Madey BMC Bioinformatics 2008, 9:15 (11 January 2008) |
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Software
SeqAn An efficient, generic C++ library for sequence analysis Andreas Döring, David Weese, Tobias Rausch, Knut Reinert BMC Bioinformatics 2008, 9:11 (9 January 2008) |
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Software
High-throughput sequence alignment using Graphics Processing Units Michael C Schatz, Cole Trapnell, Arthur L Delcher, Amitabh Varshney BMC Bioinformatics 2007, 8:474 (10 December 2007) |
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Research
Weichun Huang, Joseph R Nevins, Uwe Ohler Genome Biology 2007, 8:R225 (24 October 2007) Phylogenetic simulation of promoter evolution were used to analyze functional site turnover in regulatory sequences. |
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Research article
Aymeric Menard, Paulina de los Santos, Arnault Graindorge, Benoit Cournoyer BMC Genomics 2007, 8:308 (4 September 2007) |
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Research article
Structure and evolution of a proviral locus of Glyptapanteles indiensis bracovirus Christopher A Desjardins, Dawn E Gundersen-Rindal, Jessica B Hostetler, Luke J Tallon, Roger W Fuester, Michael C Schatz, Monica J Pedroni, Douglas W Fadrosh, Brian J Haas, Bradley S Toms, Dan Chen, Vishvanath Nene BMC Microbiology 2007, 7:61 (26 June 2007) |
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Research
Laurence Rohmer, Christine Fong, Simone Abmayr, Michael Wasnick, Theodore Larson Freeman, Matthew Radey, Tina Guina, Kerstin Svensson, Hillary S Hayden, Michael Jacobs, Larry A Gallagher, Colin Manoil, Robert K Ernst, Becky Drees, Danielle Buckley, Eric Haugen, Donald Bovee, Yang Zhou, Jean Chang, Ruth Levy, Regina Lim, Will Gillett, Don Guenthener, Allison Kang, Scott A Shaffer, Greg Taylor, Jinzhi Chen, Byron Gallis, David A D'Argenio, Mats Forsman, Maynard V Olson, David R Goodlett, Rajinder Kaul, Samuel I Miller, Mitchell J Brittnacher et al. Genome Biology 2007, 8:R102 (5 June 2007) .Sequencing of the non-pathogenic |
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Software
Hawkeye: an interactive visual analytics tool for genome assemblies Michael C Schatz, Adam M Phillippy, Ben Shneiderman, Steven L Salzberg Genome Biology 2007, 8:R34 (9 March 2007) Hawkeye is a new, freely available visual analytics tool for genome assemblies, designed to aid in identifying and correcting assembly errors. |
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Research article
Susan M Kraemer, Sue A Kyes, Gautam Aggarwal, Amy L Springer, Siri O Nelson, Zoe Christodoulou, Leia M Smith, Wendy Wang, Emily Levin, Christopher I Newbold, Peter J Myler, Joseph D Smith BMC Genomics 2007, 8:45 (7 February 2007) |
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Research
GenomeBlast: a web tool for small genome comparison Guoqing Lu, Liying Jiang, Resa MK Helikar, Thaine W Rowley, Luwen Zhang, Xianfeng Chen, Etsuko N Moriyama BMC Bioinformatics 2006, 7(Suppl 4):S18 (12 December 2006) |
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Methodology article
E Michael Gertz, Yi-Kuo Yu, Richa Agarwala, Alejandro A Schäffer, Stephen F Altschul BMC Biology 2006, 4:41 (7 December 2006) The first description is now available of the updated TBLASTN, an implementation of the BLAST search that aligns protein sequences to a translated nucleotide database, revealing the composition-based statistics that give increased accuracy and reliability.
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Research article
454 sequencing put to the test using the complex genome of barley Thomas Wicker, Edith Schlagenhauf, Andreas Graner, Timothy J Close, Beat Keller, Nils Stein BMC Genomics 2006, 7:275 (26 October 2006) |
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Software
inGeno – an integrated genome and ortholog viewer for improved genome to genome comparisons Chunguang Liang, Thomas Dandekar BMC Bioinformatics 2006, 7:461 (20 October 2006) |
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Research
Genomic analysis reveals that Pseudomonas aeruginosa virulence is combinatorial Daniel G Lee, Jonathan M Urbach, Gang Wu, Nicole T Liberati, Rhonda L Feinbaum, Sachiko Miyata, Lenard T Diggins, Jianxin He, Maude Saucier, Eric Déziel, Lisa Friedman, Li Li, George Grills, Kate Montgomery, Raju Kucherlapati, Laurence G Rahme, Frederick M Ausubel Genome Biology 2006, 7:R90 (12 October 2006) Sequencing of a highly virulent strain of |
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Software
Todd J Treangen, Xavier Messeguer BMC Bioinformatics 2006, 7:433 (5 October 2006) |
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Software
MICA: desktop software for comprehensive searching of DNA databases William A Stokes, Benjamin S Glick BMC Bioinformatics 2006, 7:427 (3 October 2006) |
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Research article
Claudia M Romero, David DeShazer, Tamara Feldblyum, Jacques Ravel, Donald Woods, H Stanley Kim, Yan Yu, Catherine M Ronning, William C Nierman BMC Genomics 2006, 7:228 (5 September 2006) |
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Research
Bob Mau, Jeremy D Glasner, Aaron E Darling, Nicole T Perna Genome Biology 2006, 7:R44 (31 May 2006) Multiple alignment of |
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Research article
Yiting Yu, H Stanley Kim, Hui Chua, Chi Lin, Siew Sim, Daoxun Lin, Alan Derr, Reinhard Engels, David DeShazer, Bruce Birren, William C Nierman, Patrick Tan BMC Microbiology 2006, 6:46 (26 May 2006) |
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Research article
Identification of consensus RNA secondary structures using suffix arrays Mohammad Anwar, Truong Nguyen, Marcel Turcotte BMC Bioinformatics 2006, 7:244 (5 May 2006) |
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Methodology article
Chaos game representation for comparison of whole genomes Jijoy Joseph, Roschen Sasikumar BMC Bioinformatics 2006, 7:243 (5 May 2006) |
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Research article
Andrew V Uzilov, Joshua M Keegan, David H Mathews BMC Bioinformatics 2006, 7:173 (27 March 2006) |
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Research article
H Chiapello, I Bourgait, F Sourivong, G Heuclin, A Gendrault-Jacquemard, M-A Petit, M El Karoui BMC Bioinformatics 2005, 6:171 (12 July 2005) |
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Research article
Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release Brian J Haas, Jennifer R Wortman, Catherine M Ronning, Linda I Hannick, Roger K Smith, Rama Maiti, Agnes P Chan, Chunhui Yu, Maryam Farzad, Dongying Wu, Owen White, Christopher D Town BMC Biology 2005, 3:7 (22 March 2005) The TIGR group explain how they reannotated the Arabidopsis genome, with several thousand new genes and pseudogenes annotated, 1/3 of the original annotations refined and every protein-coding gene assigned to a Gene Ontology term.
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Research
Serendipitous discovery of Wolbachia genomes in multiple Drosophila species Steven L Salzberg, Julie Hotopp, Arthur L Delcher, Mihai Pop, Douglas R Smith, Michael B Eisen, William C Nelson Genome Biology 2005, 6:R23 (22 February 2005) By searching the publicly available repository of DNA sequencing trace data, we discovered three new species of the bacterial endosymbiont |
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Research
Accelerated evolution associated with genome reduction in a free-living prokaryote Alexis Dufresne, Laurence Garczarek, Frédéric Partensky Genome Biology 2005, 6:R14 (14 January 2005) |