Results 11 to 20 of about 208,264 (275)

COGNATE: comparative gene annotation characterizer

BMC Genomics, 2017
Background The comparison of gene and genome structures across species has the potential to reveal major trends of genome evolution. However, such a comparative approach is currently hampered by a lack of standardization (e.g., Elliott TA, Gregory TR ...
Jeanne Wilbrandt, Bernhard Misof, Oliver Niehuis   +2 more
doaj   +4 more sources

Consistent annotation of gene expression arrays [PDF]

BMC Genomics, 2010
Background Gene expression arrays are valuable and widely used tools for biomedical research. Today's commercial arrays attempt to measure the expression level of all of the genes in the genome.
Proctor Glenn, Johnson Nathan, Ballester Benoît, Flicek Paul   +3 more
doaj   +4 more sources

Gene discovery by stringent annotation [PDF]

Genome Biology, 2001
Jonathan B Weitzman
openalex   +3 more sources

GoFigure: Automated Gene Ontology™ annotation [PDF]

Bioinformatics, 2003
Abstract Summary: We have developed a web tool to predict Gene Ontology (GO) terms. The tool accepts an input DNA or protein sequence, and uses BLAST to identify homologous sequences in GO annotated databases. A graph is returned to the user via email. Availability: The tool is freely available at: http://udgenome.ags.udel.
Salim Khan, Gang Situ, Keith Decker, Carl J. Schmidt   +3 more
openalex   +4 more sources

GeneMachine: gene prediction and sequence annotation [PDF]

Bioinformatics, 2001
Abstract Motivation: A number of free-standing programs have been developed in order to help researchers find potential coding regions and deduce gene structure for long stretches of what is essentially ‘anonymous DNA’. As these programs apply inherently different criteria to the question of what is and is not a coding region, multiple ...
Izabela Makałowska, Joseph F. Ryan, Andreas D. Baxevanis   +2 more
openalex   +4 more sources

Annotation of plasmid genes [PDF]

Plasmid, 2017
Good annotation of plasmid genomes is essential to maximise the value of the rapidly increasing volume of plasmid sequences. This short review highlights some of the current issues and suggests some ways forward. Where a well-studied related plasmid system exists we recommend that new annotation adheres to the convention already established for that ...
Eva M. Top, Laura S. Frost, Celeste J. Brown, Ana Cerdeño-Tárraga, Nicholas R. Thomson, Christopher M. Thomas   +5 more
openaire   +3 more sources

Gene Ontology Annotations and Resources [PDF]

Nucleic Acids Research, 2012
The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over the past year, the GOC has implemented several processes to increase the quantity, quality and specificity of GO annotations.
Gene Ontology Consortium, Blake, JA, Dolan, M, Drabkin, H, Hill, DP, Li, Ni, Sitnikov, D, Bridges, S, Burgess, S, Buza, T, McCarthy, F, Peddinti, D, Pillai, L, Carbon, S, Dietze, H, Ireland, A, Lewis, SE, Mungall, CJ, Gaudet, P, Chrisholm, RL, Fey, P, Kibbe, WA, Basu, S, Siegele, DA, McIntosh, BK, Renfro, DP, Zweifel, AE, Hu, JC, Brown, NH, Tweedie, S, Alam-Faruque, Y, Apweiler, R, Auchinchloss, A, Axelsen, K, Bely, B, Blatter, M-C, Bonilla, C, Bouguerleret, L, Boutet, E, Breuza, L, Bridge, A, Chan, WM, Chavali, G, Coudert, E, Dimmer, E, Estreicher, A, Famiglietti, L, Feuermann, M, Gos, A, Gruaz-Gumowski, N, Hieta, R, Hinz, C, Hulo, C, Huntley, R, James, J, Jungo, F, Keller, G, Laiho, K, Legge, D, Lemercier, P, Lieberherr, D, Magrane, M, Martin, MJ, Masson, P, Mutowo-Muellenet, P, O'Donovan, C, Pedruzzi, I, Pichler, K, Poggioli, D, Porras Millán, P, Poux, S, Rivoire, C, Roechert, B, Sawford, T, Schneider, M, Stutz, A, Sundaram, S, Tognolli, M, Xenarios, I, Foulgar, R, Lomax, J, Roncaglia, P, Khodiyar, VK, Lovering, RC, Talmud, PJ, Chibucos, M, Giglio, M Gwinn, Chang, H-Y, Hunter, S, McAnulla, C, Mitchell, A, Sangrador, A, Stephan, R, Harris, MA, Oliver, SG, Rutherford, K, Wood, V, Bahler, J, Lock, A, Kersey, PJ, McDowall, DM, Staines, DM, Dwinell, M, Shimoyama, M, Laulederkind, S, Hayman, T, Wang, S-J, Petri, V, Lowry, T, D'Eustachio, P, Matthews, L, Balakrishnan, R, Binkley, G, Cherry, JM, Costanzo, MC, Dwight, SS, Engel, SR, Fisk, DG, Hitz, BC, Hong, EL, Karra, K, Miyasato, SR, Nash, RS, Park, J, Skrzypek, MS, Weng, S, Wong, ED, Berardini, TZ, Huala, E, Mi, H, Thomas, PD, Chan, J, Kishore, R, Sternberg, P, Van Auken, K, Howe, D, Westerfield, M   +136 more
openaire   +6 more sources

The Ensembl gene annotation system [PDF]

Database, 2016
The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects. Furthermore, it generates the automatic alignment-based annotation for the human and mouse GENCODE gene sets. The system is based on the alignment of biological sequences, including cDNAs, proteins and RNA-seq reads,
Daniel N. Murphy, Susan Fairley, Fergal J. Martin, Daniel Barrell, Andreas Kähäri, Carlos García Girón, Bronwen Aken, Bronwen Aken, Amonida Zadissa, Paul Flicek, Kevin L. Howe, Simon D. M. White, Magali Ruffier, Valery Curwen, Felix Kokocinski, Konstantinos Billis, Thibaut Hourlier, Rishi Nag, Michael Schuster, Jan-Hinnerk Vogel, Laura Clarke, Stephen M. J. Searle, Y. Amy Tang, Julio Fernandez Banet, Sarah Ayling   +24 more
openaire   +4 more sources

AMIGene: Annotation of MIcrobial Genes [PDF]

Nucleic Acids Research, 2003
AMIGene (Annotation of MIcrobial Genes) is an application for automatically identifying the most likely coding sequences (CDSs) in a large contig or a complete bacterial genome sequence. The first step in AMIGene is dedicated to the construction of Markov models that fit the input genomic data (i.e.
Nuel, Gregory, Bocs, S., Cruveiller, S., Vellenet, D., Medigue, C.   +4 more
openaire   +3 more sources

Community gene annotation in practice [PDF]

Database, 2012
Manual annotation of genomic data is extremely valuable to produce an accurate reference gene set but is expensive compared with automatic methods and so has been limited to model organisms. Annotation tools that have been developed at the Wellcome Trust Sanger Institute (WTSI, http://www.sanger.ac.uk/.) are being used to fill that gap, as they can be ...
James G. R. Gilbert, Ed Griffiths, Jane E. Loveland, Jennifer Harrow   +3 more
openaire   +3 more sources