Results 21 to 30 of about 401,494 (259)

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 ...
Thomas, Christopher M, Thomson, Nicholas R, Cerdeño-Tárraga, Ana M, Brown, Celeste J, Top, Eva M, Frost, Laura S   +5 more
openaire   +2 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

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   +4 more sources

Annotation matters: the effect of structural gene annotation on orthology inference. [PDF]

Bioinformatics
Abstract Motivation In silico gene annotation, the process of identifying the genes present in a genome, remains a challenging task. As genome assemblies rapidly increase, the corresponding gene models and repertoires often fall short in quality.
Prieto-Baños S, Nevers Y, Altenhoff A, Warwick Vesztrocy A, Dessimoz C, Glover NM.   +5 more
europepmc   +5 more sources

Manual Annotation Studio (MAS): a collaborative platform for manual functional annotation of viral and microbial genomes

BMC Genomics, 2021
Background Functional genome annotation is the process of labelling functional genomic regions with descriptive information. Manual curation can produce higher quality genome annotations than fully automated methods.
Matthew R. Lueder, Regina Z. Cer, Miles Patrick, Logan J. Voegtly, Kyle A. Long, Gregory K. Rice, Kimberly A. Bishop-Lilly   +6 more
doaj   +1 more source

PINOT: an intuitive resource for integrating protein-protein interactions

Cell Communication and Signaling, 2020
Background The past decade has seen the rise of omics data for the understanding of biological systems in health and disease. This wealth of information includes protein-protein interaction (PPI) data derived from both low- and high-throughput assays ...
James E. Tomkins, Raffaele Ferrari, Nikoleta Vavouraki, John Hardy, Ruth C. Lovering, Patrick A. Lewis, Liam J. McGuffin, Claudia Manzoni   +7 more
doaj   +1 more source

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 ...
Jane E. Loveland, James G. R. Gilbert, Ed Griffiths, Jennifer L. Harrow   +3 more
openaire   +2 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,
Bronwen L. Aken, Sarah C. Ayling, Daniel Barrell, Laura Clarke, Valery Curwen, Susan Fairley, Julio Fernandez-Banet, Konstantinos Billis, Carlos García-Girón, Thibaut Hourlier, Kevin Lee Howe, Andreas Kähäri, Felix Kokocinski, Fergal J. Martin, Daniel N. Murphy, Rishi Nag, Magali Ruffier, Michael Schuster, Y. Amy Tang, Jan Vogel, Simon White, Amonida Zadissa, Paul Flicek, Stephen M. J. Searle   +23 more
openaire   +3 more sources

Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL [PDF]

Journal of Biomedical Semantics, 2012
Ontologies such as the Gene Ontology (GO) and their use in annotations make cross species comparisons of genes possible, along with a wide range of other analytical activities. The bio-ontologies community, in particular the Open Biomedical Ontologies (OBO) community, have provided many other ontologies and an increasingly large volume of annotations ...
Jupp, Simon, Stevens, Robert, Hoehndorf, Robert   +2 more
openaire   +5 more sources

A curated catalog of canine and equine keratin genes. [PDF]

PLoS ONE, 2017
Keratins represent a large protein family with essential structural and functional roles in epithelial cells of skin, hair follicles, and other organs. During evolution the genes encoding keratins have undergone multiple rounds of duplication and humans ...
Pierre Balmer, Anina Bauer, Shashikant Pujar, Kelly M McGarvey, Monika Welle, Arnaud Galichet, Eliane J Müller, Kim D Pruitt, Tosso Leeb, Vidhya Jagannathan   +9 more
doaj   +1 more source