Small Genome Annotation and Data Management at TIGR (2008)
Michelle Gwinn, William Nelson, Robert Dodson, Steven Salzberg, Owen White
TIGR has developed, and continues to refine, a comprehensive, efficient system for small genome annotation. The Glimmer gene finding software identifies open reading frames most likely to code for...
Haas, Brian J, Salzberg, Steven L, Zhu, Wei, Pertea, Mihaela, Allen, Jonathan E, Orvis, Joshua, ...
Abstract EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM,...
Haas, Brian U., Salzberg, Steven L., Zhu, Wei, Pertea, Mihaela, Allen, Jonathan E., Orvis, Joshua, ...
EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when...
Environmental Genome Shotgun Sequencing of the Sargasso Sea (2008)
Sargasso Sea, J. Craig Venter, Et Al, J. Craig Venter, Karin Remington, John F. Heidelberg, ...
The following resources related to this article are available online at
Jonathan A Eisen, John F Heidelberg, Owen White, Steven L Salzberg
for symmetric chromosomal inversions around the
Arthur L. Delcher, Simon Kasif, Robert D. Fleischmann, Jeremy Peterson, Owen White, Steven L. Salzberg
A new system for aligning whole genome sequences is described. Using an efficient data structure called a suffix tree, the system is able to rapidly align sequences containing millions of...
Arthur L. Delcher, Simon Kasif, Robert D. Fleischmann, Jeremy Peterson, Owen White, Steven L. Salzberg
A new system for aligning whole genome sequences is described. Using an efficient data structure called a suffix tree, the system is able to rapidly align sequences containing millions of...
Genome Sequence of Babesia bovis and Comparative Analysis of Apicomplexan Hemoprotozoa (2007)
Kelly A. Brayton, David R. Herndon, Linda Hannick, Lowell S. Kappmeyer, Shawn J. Berens, ...
Babesia bovis is an apicomplexan tick-transmitted pathogen of cattle imposing a global risk and severe constraints to livestock health and economic development. The complete genome sequence was...
Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis (2007)
Carlton, Jane M., Hirt, Robert P., Silva, Joana C., Delcher, Arthur L., Schatz, Michael, Zhao, Qi, ...
We describe the genome sequence of the protist Trichomonas vaginalis, a sexually transmitted human pathogen. Repeats and transposable elements comprise about two-thirds of the ~160-megabase genome,...
Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis (2007)
Carlton, Jane M., Hirt, Robert ., Silva, Joana C., Delcher, Arthur L., Schatz, Michael, Zhao, Qi, ...
We describe the genome sequence of the protist Trichomonas vaginalis, a sexually transmitted human pathogen. Repeats and transposable elements comprise about two-thirds of the similar to 160-megabase...
Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis (2007)
Carlton, Jane M., Hirt, Robert ., Silva, Joana C., Delcher, Arthur L., Schatz, Michael, Zhao, Qi, ...
We describe the genome sequence of the protist Trichomonas vaginalis, a sexually transmitted human pathogen. Repeats and transposable elements comprise about two-thirds of the similar to 160-megabase...
Selengut, Jeremy D., Haft, Daniel H., Davidsen, Tanja, Ganapathy, Anurhada, Gwinn-Giglio, Michelle, Nelson, William C., ...
TIGRFAMs is a collection of protein family definitions built to aid in high-throughput annotation of specific protein functions. Each family is based on a hidden Markov model (HMM), where both cutoff...
Correction: Comparative Genomics of Emerging Human Ehrlichiosis Agents (2006)
Mingqun Lin, Ramana Madupu, Jonathan Crabtree, Samuel V. Angiuoli, Jonathan A. Eisen, ...
Comparative Genomics of Emerging Human Ehrlichiosis Agents (2006)
Mingqun Lin, Ramana Madupu, Jonathan Crabtree, Samuel V. Angiuoli, Jonathan Eisen, ...
Anaplasma (formerly Ehrlichia) phagocytophilum, Ehrlichia chaffeensis, and Neorickettsia (formerly Ehrlichia) sennetsu are intracellular vector-borne pathogens that cause human ehrlichiosis, an...
TIGRFAMs and Genome Properties: tools for the (2006)
Jeremy D. Selengut, Daniel H. Haft, Tanja Davidsen, Anurhada Ganapathy, Michelle Gwinn-giglio, William C. Nelson, ...
assignment of molecular function and biological process in prokaryotic genomes
Selengut, Jeremy D., Haft, Daniel H., Davidsen, Tanja, Ganapathy, Anurhada, Gwinn-Giglio, Michelle, Nelson, William C., ...
TIGRFAMs is a collection of protein family definitions built to aid in high-throughput annotation of specific protein functions. Each family is based on a hidden Markov model (HMM), where both cutoff...
Selengut, Jeremy D., Haft, Daniel H., Davidsen, Tanja, Ganapathy, Anurhada, Gwinn-Giglio, Michelle, Nelson, William C., ...
TIGRFAMs is a collection of protein family definitions built to aid in high-throughput annotation of specific protein functions. Each family is based on a hidden Markov model (HMM), where both cutoff...
Haas, Brian J, Wortman, Jennifer R, Ronning, Catherine M, Hannick, Linda I, Smith, Roger K, Maiti, Rama, ...
Abstract Background Since the initial publication of its complete genome sequence, Arabidopsis thaliana has become more important than ever as a model for plant research. However, the initial genome...
Networking: Freemasons and the Colonial State in French West Africa, 1895-1914 (2005)
The links between freemasons and republican elites in late nineteenth- and early twentieth-century France are well known to historians, but despite recent discussion of a distinctively republican...
Haft, Daniel H., Selengut, Jeremy D., Brinkac, Lauren M., Zafar, Nikhat, White, Owen
Motivation: The presence or absence of metabolic pathways and structures provide a context that makes protein annotation far more reliable. Compiling such information across microbial genomes...
Bishop, Richard, Shah, Trushar, Pelle, Roger, Hoyle, David, Pearson, Terry, Haines, Lee, ...
Massively parallel signature sequencing (MPSS) was used to analyze the transcriptome of the intracellular protozoan Theileria parva. In total 1 095 000, 20 bp sequences representing 4371...
Haft, Daniel H., Selengut, Jeremy D., Brinkac, Lauren M., Zafar, Nikhat, White, Owen
Motivation: The presence or absence of metabolic pathways, and structures provides context that makes protein annotation far more reliable. Compiling such information across microbial genomes...
Nelson, Karen E., Fouts, Derrick E., Mongodin, Emmanuel F., Ravel, Jacques, DeBoy, Robert T., Kolonay, James F., ...
The genomes of three strains of Listeria monocytogenes that have been associated with food‐borne illness in the USA were subjected to whole genome comparative analysis. A total of 51, 97 and 69...
Haft, Daniel H., Selengut, Jeremy D., Brinkac, Lauren M., Zafar, Nikhat, White, Owen
Motivation: The presence or absence of metabolic pathways, and structures provides context that makes protein annotation far more reliable. Compiling such information across microbial genomes...
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies (2003)
Haas, Brian J., Delcher, Arthur L., Mount, Stephen M., Wortman, Jennifer R., Smith, Roger K., Hannick, Linda I., ...
The spliced alignment of expressed sequence data to genomic sequence has proven a key tool in the comprehensive annotation of genes in eukaryotic genomes. A novel algorithm was developed to assemble...
The sequence and analysis of Trypanosoma brucei chromosome II (2003)
Ghedin, Elodie, Song, Jinming, MacLeod, Annette, Bringaud, Frederic, Larkin, Christopher, ...
We report here the sequence of chromosome II from Trypanosoma brucei, the causative agent of African sleeping sickness. The 1.2‐Mb pairs encode about 470 predicted genes organised in 17...
The TIGRFAMs database of protein families (2003)
Haft, Daniel H., Selengut, Jeremy D., White, Owen
TIGRFAMs is a collection of manually curated protein families consisting of hidden Markov models (HMMs), multiple sequence alignments, commentary, Gene Ontology (GO) assignments, literature...
Full-length messenger RNA sequences greatly improve genome annotation (2002)
Haas, Brian J, Volfovsky, Natalia, Town, Christopher D, Troukhan, Maxim, Alexandrov, Nickolai, Feldmann, Kenneth A, ...
Abstract Background Annotation of eukaryotic genomes is a complex endeavor that requires the integration of evidence from multiple, often contradictory, sources. With the ever-increasing amount of...
Full-length messenger RNA sequences greatly improve genome annotation (2002)
Haas, Brian J, Volfovsky, Natalia, Town, Christopher D, Troukhan, Maxim, Alexandrov, Nickolai, Feldman, Kenneth A, ...
Background: Annotation of eukaryotic genomes is a complex endeavor that requires the integration of evidence from multiple, often contradictory, sources. With the ever-increasing amount of genome...
DOI: 10.1093/nar/gkg128 The TIGRFAMs database of protein families (2002)
Daniel H. Haft, Jeremy D. Selengut, Owen White
TIGRFAMs is a collection of manually curated protein families consisting of hidden Markov models (HMMs), multiple sequence alignments, commentary, Gene Ontology (GO) assignments, literature...
Prediction of operons in microbial genomes (2001)
Maria D. Ermolaeva, Owen White, Steven L. Salzberg
Operon structure is an important organization feature of bacterial genomes. Many sets of genes occur in the same order on multiple genomes; these conserved gene groupings represent candidate operons....
The Comprehensive Microbial Resource (2001)
Peterson, Jeremy D., Umayam, Lowell A., Dickinson, Tanja, Hickey, Erin K., White, Owen
One challenge presented by large-scale genome sequencing efforts is effective display of uniform information to the scientific community. The Comprehensive Microbial Resource (CMR) contains robust...
TIGRFAMs: a protein family resource for the functional identification of proteins (2001)
Haft, Daniel H., Loftus, Brendan J., Richardson, Delwood L., Yang, Fan, Eisen, Jonathan A., Paulsen, Ian T., ...
TIGRFAMs is a collection of protein families featuring curated multiple sequence alignments, hidden Markov models and associated information designed to support the automated functional...
Prediction of operons in microbial genomes (2001)
Ermolaeva, Maria D., White, Owen, Salzberg, Steven L.
Operon structure is an important organization feature of bacterial genomes. Many sets of genes occur in the same order on multiple genomes; these conserved gene groupings represent candidate operons....
Evidence for symmetric chromosomal inversions around the replication origin in bacteria (2000)
Eisen, Jonathan A, Heidelberg, John F, White, Owen, Salzberg, Steven L
Abstract Background Whole-genome comparisons can provide great insight into many aspects of biology. Until recently, however, comparisons were mainly possible only between distantly related species....
Evidence for symmetric chromosomal inversions around the replication origin in bacteria (2000)
Eisen, Jonathan A., Heidelberg, John F., White, Owen, Salzberg, Steven L.
Background: Whole-genome comparisons can provide great insight into many aspects of biology. Until recently, however, comparisons were mainly possible only between distantly related species. Complete...
Prediction of Transcription Terminators in Bacterial Genomes (2000)
Maria D. Ermolaeva, Hanif G. Khalak, Owen White, Hamilton O. Smith, Steven L. Salzberg
Introduction Bacterial genomes are organized into units of expression that are bounded by sites where transcription of DNA into RNA is initiated and terminated. Regulation of gene expression is often...
Microbial gene identification using interpolated Markov models (1998)
Steven L. Salzberg, Arthur L. Delcher, Simon Kasif, Owen White
This paper describes a new system, GLIMMER, for finding genes in microbial genomes. In a series of tests on Haemophilus influenzae, Helicobacter pylori and other complete microbial genomes, this...
Microbial gene identification using interpolated Markov models (1998)
Steven L. Salzberg, Arthur L. Delcher, Simon Kasif, Owen White
This paper describes a new system, GLIMMER, for finding genes in microbial genomes. In a series of tests on Haemophilus influenzae, Helicobacter pylori and other complete microbial genomes, this...
Microbial gene identification using interpolated Markov models (1998)
Steven L. Salzberg, Arthur L. Delcher, Simon Kasif, Owen White
This paper describes a new system, GLIMMER, for finding genes in microbial genomes. In a series of tests on Haemophilus influenzae, Helicobacter pylori and other complete microbial genomes, this...
Miscegenation and colonial society in French West Africa, c.1900-1960 /--Owen White. (1996)
"Thesis number D192365."
Miscegenation and colonial society in French West Africa c.1900-1960 [microform] / (1996)
BLDSC reference no.: D192365.
A rapid retrieval tool for operating on large, flat archive files (1995)
Computer-aided sequencing and analysis facilities need to efficiently search flat archive files. Retrieval by e-mail or network server connections can become impractical in cases where large numbers...
A quality control algorithm for DNA sequencing projects (1993)
White, Owen, Dunning, Ted, Sutton, Granger, Adams, Mark, Venter, J. Craig, Fields, Chris
Heterologous DNA sequences from rearrangements with the genomes of host cells, genomic fragments from hybrid cells, or impure tissue sources can threaten the purity of libraries that are derived from...
Splicing signals in Drosophila: intron size, information content, and consensus sequences (1992)
Mount, Stephen M., Burks, Christian, Herts, Gerald, Stormo, Gary D., White, Owen, Fields, Chris
A database of 209 Drosophila Introns was extracted from Genbank (release number 64.0) and examined by a number of methods in order to characterize features that might serve as signals for messenger...
Evidence for symmetric chromosomal inversions around the replication origin in bacteria
Eisen, Jonathan A, Heidelberg, John F, White, Owen, Salzberg, Steven L
Prediction of operons in microbial genomes
Ermolaeva, Maria D., White, Owen, Salzberg, Steven L.
Operon structure is an important organization feature of bacterial genomes. Many sets of genes occur in the same order on multiple genomes; these conserved gene groupings represent candidate operons....
TIGRFAMs: a protein family resource for the functional identification of proteins
Haft, Daniel H., Loftus, Brendan J., Richardson, Delwood L., Yang, Fan, Eisen, Jonathan A., Paulsen, Ian T., ...
TIGRFAMs is a collection of protein families featuring curated multiple sequence alignments, hidden Markov models and associated information designed to support the automated functional...
The Comprehensive Microbial Resource
Peterson, Jeremy D., Umayam, Lowell A., Dickinson, Tanja, Hickey, Erin K., White, Owen
One challenge presented by large-scale genome sequencing efforts is effective display of uniform information to the scientific community. The Comprehensive Microbial Resource (CMR) contains robust...
Complete genome sequence of Caulobacter crescentus
Nierman, William C., Feldblyum, Tamara V., Laub, Michael T., Paulsen, Ian T., Nelson, Karen E., Eisen, Jonathan, ...
The complete genome sequence of Caulobacter crescentus was determined to be 4,016,942 base pairs in a single circular chromosome encoding 3,767 genes. This organism, which grows in a dilute aquatic...
Full-length messenger RNA sequences greatly improve genome annotation
Haas, Brian J, Volfovsky, Natalia, Town, Christopher D, Troukhan, Maxim, Alexandrov, Nickolai, Feldmann, Kenneth A, ...
Eisen, Jonathan A., Nelson, Karen E., Paulsen, Ian T., Heidelberg, John F., Wu, Martin, Dodson, Robert J., ...
The complete genome of the green-sulfur eubacterium Chlorobium tepidum TLS was determined to be a single circular chromosome of 2,154,946 bp. This represents the first genome sequence from the phylum...
Paulsen, Ian T., Seshadri, Rekha, Nelson, Karen E., Eisen, Jonathan A., Heidelberg, John F., Read, Timothy D., ...
The 3.31-Mb genome sequence of the intracellular pathogen and potential bioterrorism agent, Brucella suis, was determined. Comparison of B. suis with Brucella melitensis has defined a finite set of...
The TIGRFAMs database of protein families
Haft, Daniel H., Selengut, Jeremy D., White, Owen
TIGRFAMs is a collection of manually curated protein families consisting of hidden Markov models (HMMs), multiple sequence alignments, commentary, Gene Ontology (GO) assignments, literature...
The sequence and analysis of Trypanosoma brucei chromosome II
Ghedin, Elodie, Song, Jinming, MacLeod, Annette, Bringaud, Frederic, Larkin, Christopher, ...
We report here the sequence of chromosome II from Trypanosoma brucei, the causative agent of African sleeping sickness. The 1.2-Mb pairs encode about 470 predicted genes organised in 17 directional...
Miller, Eric S., Heidelberg, John F., Eisen, Jonathan A., Nelson, William C., Durkin, A. Scott, Ciecko, Ann, ...
The complete genome sequence of the T4-like, broad-host-range vibriophage KVP40 has been determined. The genome sequence is 244,835 bp, with an overall G+C content of 42.6%. It encodes 386 putative...
The Genome of M. acetivorans Reveals Extensive Metabolic and Physiological Diversity
Galagan, James E., Nusbaum, Chad, Roy, Alice, Endrizzi, Matthew G., Macdonald, Pendexter, FitzHugh, Will, ...
Methanogenesis, the biological production of methane, plays a pivotal role in the global carbon cycle and contributes significantly to global warming. The majority of methane in nature is derived...
Buell, C. Robin, Joardar, Vinita, Lindeberg, Magdalen, Selengut, Jeremy, Paulsen, Ian T., Gwinn, Michelle L., ...
We report the complete genome sequence of the model bacterial pathogen Pseudomonas syringae pathovar tomato DC3000 (DC3000), which is pathogenic on tomato and Arabidopsis thaliana. The DC3000 genome...
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies
Haas, Brian J., Delcher, Arthur L., Mount, Stephen M., Wortman, Jennifer R., Smith, Roger K., Hannick, Linda I., ...
The spliced alignment of expressed sequence data to genomic sequence has proven a key tool in the comprehensive annotation of genes in eukaryotic genomes. A novel algorithm was developed to assemble...
Nelson, Karen E., Fouts, Derrick E., Mongodin, Emmanuel F., Ravel, Jacques, DeBoy, Robert T., Kolonay, James F., ...
The genomes of three strains of Listeria monocytogenes that have been associated with food-borne illness in the USA were subjected to whole genome comparative analysis. A total of 51, 97 and 69...
Structural flexibility in the Burkholderia mallei genome
Nierman, William C., DeShazer, David, Kim, H. Stanley, Tettelin, Herve, Nelson, Karen E., Feldblyum, Tamara, ...
The complete genome sequence of Burkholderia mallei ATCC 23344 provides insight into this highly infectious bacterium's pathogenicity and evolutionary history. B. mallei, the etiologic agent of...
Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release
Haas, Brian J, Wortman, Jennifer R, Ronning, Catherine M, Hannick, Linda I, Smith, Roger K, Maiti, Rama, ...
Tettelin, Hervé, Masignani, Vega, Cieslewicz, Michael J., Donati, Claudio, Medini, Duccio, Ward, Naomi L., ...
The development of efficient and inexpensive genome sequencing methods has revolutionized the study of human bacterial pathogens and improved vaccine design. Unfortunately, the sequence of a single...
Joardar, Vinita, Lindeberg, Magdalen, Jackson, Robert W., Selengut, Jeremy, Dodson, Robert, Brinkac, Lauren M., ...
Pseudomonas syringae pv. phaseolicola, a gram-negative bacterial plant pathogen, is the causal agent of halo blight of bean. In this study, we report on the genome sequence of P. syringae pv....
Bishop, Richard, Shah, Trushar, Pelle, Roger, Hoyle, David, Pearson, Terry, Haines, Lee, ...
Massively parallel signature sequencing (MPSS) was used to analyze the transcriptome of the intracellular protozoan Theileria parva. In total 1 095 000, 20 bp sequences representing 4371...
Comparative Genomics of Emerging Human Ehrlichiosis Agents
Dunning Hotopp, Julie C., Lin, Mingqun, Madupu, Ramana, Crabtree, Jonathan, Angiuoli, Samuel V, Eisen, Jonathan, ...
Anaplasma (formerly Ehrlichia) phagocytophilum, Ehrlichia chaffeensis, and Neorickettsia (formerly Ehrlichia) sennetsu are intracellular vector-borne pathogens that cause human ehrlichiosis, an...
Evidence for symmetric chromosomal inversions around the replication origin in bacteria
Eisen, Jonathan A, Heidelberg, John F, White, Owen, Salzberg, Steven L
Prediction of operons in microbial genomes
Ermolaeva, Maria D., White, Owen, Salzberg, Steven L.
Operon structure is an important organization feature of bacterial genomes. Many sets of genes occur in the same order on multiple genomes; these conserved gene groupings represent candidate operons....
TIGRFAMs: a protein family resource for the functional identification of proteins
Haft, Daniel H., Loftus, Brendan J., Richardson, Delwood L., Yang, Fan, Eisen, Jonathan A., Paulsen, Ian T., ...
TIGRFAMs is a collection of protein families featuring curated multiple sequence alignments, hidden Markov models and associated information designed to support the automated functional...
The Comprehensive Microbial Resource
Peterson, Jeremy D., Umayam, Lowell A., Dickinson, Tanja, Hickey, Erin K., White, Owen
One challenge presented by large-scale genome sequencing efforts is effective display of uniform information to the scientific community. The Comprehensive Microbial Resource (CMR) contains robust...
Complete genome sequence of Caulobacter crescentus
Nierman, William C., Feldblyum, Tamara V., Laub, Michael T., Paulsen, Ian T., Nelson, Karen E., Eisen, Jonathan, ...
The complete genome sequence of Caulobacter crescentus was determined to be 4,016,942 base pairs in a single circular chromosome encoding 3,767 genes. This organism, which grows in a dilute aquatic...
Full-length messenger RNA sequences greatly improve genome annotation
Haas, Brian J, Volfovsky, Natalia, Town, Christopher D, Troukhan, Maxim, Alexandrov, Nickolai, Feldmann, Kenneth A, ...
Eisen, Jonathan A., Nelson, Karen E., Paulsen, Ian T., Heidelberg, John F., Wu, Martin, Dodson, Robert J., ...
The complete genome of the green-sulfur eubacterium Chlorobium tepidum TLS was determined to be a single circular chromosome of 2,154,946 bp. This represents the first genome sequence from the phylum...
Paulsen, Ian T., Seshadri, Rekha, Nelson, Karen E., Eisen, Jonathan A., Heidelberg, John F., Read, Timothy D., ...
The 3.31-Mb genome sequence of the intracellular pathogen and potential bioterrorism agent, Brucella suis, was determined. Comparison of B. suis with Brucella melitensis has defined a finite set of...
The TIGRFAMs database of protein families
Haft, Daniel H., Selengut, Jeremy D., White, Owen
TIGRFAMs is a collection of manually curated protein families consisting of hidden Markov models (HMMs), multiple sequence alignments, commentary, Gene Ontology (GO) assignments, literature...
The sequence and analysis of Trypanosoma brucei chromosome II
Ghedin, Elodie, Song, Jinming, MacLeod, Annette, Bringaud, Frederic, Larkin, Christopher, ...
We report here the sequence of chromosome II from Trypanosoma brucei, the causative agent of African sleeping sickness. The 1.2-Mb pairs encode about 470 predicted genes organised in 17 directional...
Miller, Eric S., Heidelberg, John F., Eisen, Jonathan A., Nelson, William C., Durkin, A. Scott, Ciecko, Ann, ...
The complete genome sequence of the T4-like, broad-host-range vibriophage KVP40 has been determined. The genome sequence is 244,835 bp, with an overall G+C content of 42.6%. It encodes 386 putative...
The Genome of M. acetivorans Reveals Extensive Metabolic and Physiological Diversity
Galagan, James E., Nusbaum, Chad, Roy, Alice, Endrizzi, Matthew G., Macdonald, Pendexter, FitzHugh, Will, ...
Methanogenesis, the biological production of methane, plays a pivotal role in the global carbon cycle and contributes significantly to global warming. The majority of methane in nature is derived...
Buell, C. Robin, Joardar, Vinita, Lindeberg, Magdalen, Selengut, Jeremy, Paulsen, Ian T., Gwinn, Michelle L., ...
We report the complete genome sequence of the model bacterial pathogen Pseudomonas syringae pathovar tomato DC3000 (DC3000), which is pathogenic on tomato and Arabidopsis thaliana. The DC3000 genome...
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies
Haas, Brian J., Delcher, Arthur L., Mount, Stephen M., Wortman, Jennifer R., Smith, Roger K., Hannick, Linda I., ...
The spliced alignment of expressed sequence data to genomic sequence has proven a key tool in the comprehensive annotation of genes in eukaryotic genomes. A novel algorithm was developed to assemble...
Nelson, Karen E., Fouts, Derrick E., Mongodin, Emmanuel F., Ravel, Jacques, DeBoy, Robert T., Kolonay, James F., ...
The genomes of three strains of Listeria monocytogenes that have been associated with food-borne illness in the USA were subjected to whole genome comparative analysis. A total of 51, 97 and 69...
Structural flexibility in the Burkholderia mallei genome
Nierman, William C., DeShazer, David, Kim, H. Stanley, Tettelin, Herve, Nelson, Karen E., Feldblyum, Tamara, ...
The complete genome sequence of Burkholderia mallei ATCC 23344 provides insight into this highly infectious bacterium's pathogenicity and evolutionary history. B. mallei, the etiologic agent of...
Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release
Haas, Brian J, Wortman, Jennifer R, Ronning, Catherine M, Hannick, Linda I, Smith, Roger K, Maiti, Rama, ...
Tettelin, Hervé, Masignani, Vega, Cieslewicz, Michael J., Donati, Claudio, Medini, Duccio, Ward, Naomi L., ...
The development of efficient and inexpensive genome sequencing methods has revolutionized the study of human bacterial pathogens and improved vaccine design. Unfortunately, the sequence of a single...
Joardar, Vinita, Lindeberg, Magdalen, Jackson, Robert W., Selengut, Jeremy, Dodson, Robert, Brinkac, Lauren M., ...
Pseudomonas syringae pv. phaseolicola, a gram-negative bacterial plant pathogen, is the causal agent of halo blight of bean. In this study, we report on the genome sequence of P. syringae pv....
Bishop, Richard, Shah, Trushar, Pelle, Roger, Hoyle, David, Pearson, Terry, Haines, Lee, ...
Massively parallel signature sequencing (MPSS) was used to analyze the transcriptome of the intracellular protozoan Theileria parva. In total 1 095 000, 20 bp sequences representing 4371...
Comparative Genomics of Emerging Human Ehrlichiosis Agents
Dunning Hotopp, Julie C., Lin, Mingqun, Madupu, Ramana, Crabtree, Jonathan, Angiuoli, Samuel V, Eisen, Jonathan, ...
Anaplasma (formerly Ehrlichia) phagocytophilum, Ehrlichia chaffeensis, and Neorickettsia (formerly Ehrlichia) sennetsu are intracellular vector-borne pathogens that cause human ehrlichiosis, an...
Correction: Comparative Genomics of Emerging Human Ehrlichiosis Agents
Dunning Hotopp, Julie C, Lin, Mingqun, Madupu, Ramana, Crabtree, Jonathan, Angiuoli, Samuel V, Eisen, Jonathan A, ...
Selengut, Jeremy D., Haft, Daniel H., Davidsen, Tanja, Ganapathy, Anurhada, Gwinn-Giglio, Michelle, Nelson, William C., ...
TIGRFAMs is a collection of protein family definitions built to aid in high-throughput annotation of specific protein functions. Each family is based on a hidden Markov model (HMM), where both cutoff...
Heinicke, Sven, Livstone, Michael S., Lu, Charles, Oughtred, Rose, Kang, Fan, Angiuoli, Samuel V., ...
Many biological databases that provide comparative genomics information and tools are now available on the internet. While certainly quite useful, to our knowledge none of the existing databases...
Genome Sequence of Babesia bovis and Comparative Analysis of Apicomplexan Hemoprotozoa
Brayton, Kelly A, Lau, Audrey O. T, Herndon, David R, Hannick, Linda, Kappmeyer, Lowell S, Berens, Shawn J, ...
Babesia bovis is an apicomplexan tick-transmitted pathogen of cattle imposing a global risk and severe constraints to livestock health and economic development. The complete genome sequence was...
Greene, John M., Collins, Frank, Lefkowitz, Elliot J., Roos, David, Scheuermann, Richard H., Sobral, Bruno, ...
Haas, Brian J, Salzberg, Steven L, Zhu, Wei, Pertea, Mihaela, Allen, Jonathan E, Orvis, Joshua, ...
EVidenceModeler (EVM) is an automated annotation tool that predicts protein-coding regions, alternatively spliced transcripts and untranslated regions of eukaryotic genes.