Results 31 to 40 of about 37,620 (216)

A software framework for microarray and gene expression object model (MAGE-OM) array design annotation [PDF]

, 2008
Background The MIAME and MAGE-OM standards defined by the MGED society provide a specification and implementation of a software infrastructure to facilitate the submission and sharing of data from microarray studies via public repositories.
Ivens Alasdair, Ivens, Alasdair, Qureshi, Matloob, Matloob Qureshi, Alasdair Ivens, Matloob Qureshi, Qureshi Matloob   +6 more
core   +1 more source

CANT-HYD: A Curated Database of Phylogeny-Derived Hidden Markov Models for Annotation of Marker Genes Involved in Hydrocarbon Degradation

Frontiers in Microbiology, 2022
Many pathways for hydrocarbon degradation have been discovered, yet there are no dedicated tools to identify and predict the hydrocarbon degradation potential of microbial genomes and metagenomes.
Varada Khot, Jackie Zorz, Daniel A. Gittins, Anirban Chakraborty, Emma Bell, María A. Bautista, Alexandre J. Paquette, Alyse K. Hawley, Breda Novotnik, Casey R. J. Hubert, Marc Strous, Srijak Bhatnagar   +11 more
doaj   +1 more source

EuCAP, a Eukaryotic Community Annotation Package, and its application to the rice genome

BMC Genomics, 2007
Background Despite the improvements of tools for automated annotation of genome sequences, manual curation at the structural and functional level can provide an increased level of refinement to genome annotation.
Hamilton John P, Campbell Matthew, Thibaud-Nissen Françoise, Zhu Wei, Buell C   +4 more
doaj   +1 more source

Non‐homology‐based prediction of gene functions in maize (Zea mays ssp. mays)

The Plant Genome, 2020
Advances in genome sequencing and annotation have eased the difficulty of identifying new gene sequences. Predicting the functions of these newly identified genes remains challenging.
Xiuru Dai, Zheng Xu, Zhikai Liang, Xiaoyu Tu, Silin Zhong, James C. Schnable, Pinghua Li   +6 more
doaj   +1 more source

Discovery of a Novel Intron in US10/US11/US12 of HSV-1 Strain 17

Viruses, 2023
Herpes Simplex Virus type 1 (HSV-1) infects humans and causes a variety of clinical manifestations. Many HSV-1 genomes have been sequenced with high-throughput sequencing technologies and the annotation of these genome sequences heavily relies on the ...
Weizhong Chang, Ming Hao, Ju Qiu, Brad T. Sherman, Tomozumi Imamichi   +4 more
doaj   +1 more source

Annotation extension through protein family annotation coherence metrics

Frontiers in Genetics, 2013
Protein functional annotation consists in associating proteins with textual descriptors elucidating their biological roles. The bulk of annotation is done via automated procedures that ultimately rely on annotation transfer.
Hugo Paulo Bastos, Luka Alexander Clarke, Francisco eCouto   +2 more
doaj   +1 more source

A novel Modulator of Ring Stage Translation (MRST) gene alters artemisinin sensitivity in Plasmodium falciparum

mSphere, 2023
The implementation of artemisinin (ART) combination therapies (ACTs) has greatly decreased deaths caused by Plasmodium falciparum malaria, but increasing ACT resistance in Southeast Asia and Africa could reverse this progress. Parasite population genetic
Caroline Simmons, Justin Gibbons, Chengqi Wang, Camilla Valente Pires, Min Zhang, Faiza Siddiqui, Jenna Oberstaller, Debora Casandra, Andreas Seyfang, Liwang Cui, Thomas D. Otto, John H. Adams   +11 more
doaj   +1 more source

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   +1 more source

Chromosome-level genome assembly of Fragaria pentaphylla using PacBio and Hi-C technologies

Frontiers in Genetics, 2022
Fragaria pentaphylla, a wild diploid quinquefoliolate species of Fragaria, is native to Southwest China. It has two morphs of red and white fruit color in nature and has characteristics of unique fragrance and resistance, which made it not only a ...
Rui Sun, Rui Sun, Rui Sun, Shuangtao Li, Shuangtao Li, Shuangtao Li, Linlin Chang, Linlin Chang, Linlin Chang, Jing Dong, Jing Dong, Jing Dong, Chuanfei Zhong, Chuanfei Zhong, Chuanfei Zhong, Hongli Zhang, Hongli Zhang, Hongli Zhang, Lingzhi Wei, Lingzhi Wei, Lingzhi Wei, Yongshun Gao, Yongshun Gao, Yongshun Gao, Guixia Wang, Guixia Wang, Guixia Wang, Yuntao Zhang, Yuntao Zhang, Yuntao Zhang, Jian Sun, Jian Sun, Jian Sun   +32 more
doaj   +1 more source

Prosecutor: parameter-free inference of gene function for prokaryotes using DNA microarray data, genomic context and multiple gene annotation sources [PDF]

, 2008
Background: Despite a plethora of functional genomic efforts, the function of many genes in sequenced genomes remains unknown. The increasing amount of microarray data for many species allows employing the guilt-by-association principle to predict ...
Hofstede, K.J., Oscar P Kuipers, Hijum, Sacha A.F.T. van,, Breitling, Rainer, Blom, E.J., Breitling, R., Breitling, Rainer,, Blom Evert, Roerdink, J.B.T.M., Hofstede Klaas, Breitling Rainer, Jos BTM Roerdink, Blom, Evert Jan, Klaas Hofstede, Roerdink, J.B.T.M.; id_orcid, Kuipers, Oscar P.,, van Hijum, S.A F T, Kuipers, O.P., Hofstede, Klaas Jan,, Roerdink, Jos B T M, van Hijum Sacha AFT, Roerdink Jos BTM, Kuipers, Oscar P., Rainer Breitling, van Hijum, S.A.F.T., Kuipers Oscar P, Hofstede, Klaas Jan, van Hijum, Sacha A F T, Blom, Evert Jan,, Sacha AFT van Hijum, Roerdink, Jos B.T.M.,, Evert Blom, Kuipers, O.P.; id_orcid   +32 more
core   +1 more source