239 related articles for article (PubMed ID: 29884752)
1. Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation.
Fiddes IT; Armstrong J; Diekhans M; Nachtweide S; Kronenberg ZN; Underwood JG; Gordon D; Earl D; Keane T; Eichler EE; Haussler D; Stanke M; Paten B
Genome Res; 2018 Jul; 28(7):1029-1038. PubMed ID: 29884752
[TBL] [Abstract][Full Text] [Related]
2. A comparative analysis of methods for de novo assembly of hymenopteran genomes using either haploid or diploid samples.
Yahav T; Privman E
Sci Rep; 2019 Apr; 9(1):6480. PubMed ID: 31019201
[TBL] [Abstract][Full Text] [Related]
3. Optimization of de novo transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms.
Haznedaroglu BZ; Reeves D; Rismani-Yazdi H; Peccia J
BMC Bioinformatics; 2012 Jul; 13():170. PubMed ID: 22808927
[TBL] [Abstract][Full Text] [Related]
4. A linked-read approach to museomics: Higher quality de novo genome assemblies from degraded tissues.
Colella JP; Tigano A; MacManes MD
Mol Ecol Resour; 2020 Jul; 20(4):856-870. PubMed ID: 32153100
[TBL] [Abstract][Full Text] [Related]
5. Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes.
Shafin K; Pesout T; Lorig-Roach R; Haukness M; Olsen HE; Bosworth C; Armstrong J; Tigyi K; Maurer N; Koren S; Sedlazeck FJ; Marschall T; Mayes S; Costa V; Zook JM; Liu KJ; Kilburn D; Sorensen M; Munson KM; Vollger MR; Monlong J; Garrison E; Eichler EE; Salama S; Haussler D; Green RE; Akeson M; Phillippy A; Miga KH; Carnevali P; Jain M; Paten B
Nat Biotechnol; 2020 Sep; 38(9):1044-1053. PubMed ID: 32686750
[TBL] [Abstract][Full Text] [Related]
6. MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects.
Holt C; Yandell M
BMC Bioinformatics; 2011 Dec; 12():491. PubMed ID: 22192575
[TBL] [Abstract][Full Text] [Related]
7. High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource.
Seaver SM; Gerdes S; Frelin O; Lerma-Ortiz C; Bradbury LM; Zallot R; Hasnain G; Niehaus TD; El Yacoubi B; Pasternak S; Olson R; Pusch G; Overbeek R; Stevens R; de Crécy-Lagard V; Ware D; Hanson AD; Henry CS
Proc Natl Acad Sci U S A; 2014 Jul; 111(26):9645-50. PubMed ID: 24927599
[TBL] [Abstract][Full Text] [Related]
8. Annotation of Full-Length Long Noncoding RNAs with Capture Long-Read Sequencing (CLS).
Carbonell Sala S; Uszczyńska-Ratajczak B; Lagarde J; Johnson R; Guigó R
Methods Mol Biol; 2021; 2254():133-159. PubMed ID: 33326074
[TBL] [Abstract][Full Text] [Related]
9. Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from non-model organisms.
Speiser DI; Pankey MS; Zaharoff AK; Battelle BA; Bracken-Grissom HD; Breinholt JW; Bybee SM; Cronin TW; Garm A; Lindgren AR; Patel NH; Porter ML; Protas ME; Rivera AS; Serb JM; Zigler KS; Crandall KA; Oakley TH
BMC Bioinformatics; 2014 Nov; 15(1):350. PubMed ID: 25407802
[TBL] [Abstract][Full Text] [Related]
10. Twelve quick steps for genome assembly and annotation in the classroom.
Jung H; Ventura T; Chung JS; Kim WJ; Nam BH; Kong HJ; Kim YO; Jeon MS; Eyun SI
PLoS Comput Biol; 2020 Nov; 16(11):e1008325. PubMed ID: 33180771
[TBL] [Abstract][Full Text] [Related]
11. RGAAT: A Reference-based Genome Assembly and Annotation Tool for New Genomes and Upgrade of Known Genomes.
Liu W; Wu S; Lin Q; Gao S; Ding F; Zhang X; Aljohi HA; Yu J; Hu S
Genomics Proteomics Bioinformatics; 2018 Oct; 16(5):373-381. PubMed ID: 30583062
[TBL] [Abstract][Full Text] [Related]
12. Considering transposable element diversification in de novo annotation approaches.
Flutre T; Duprat E; Feuillet C; Quesneville H
PLoS One; 2011 Jan; 6(1):e16526. PubMed ID: 21304975
[TBL] [Abstract][Full Text] [Related]
13. Comparison of RefSeq protein-coding regions in human and vertebrate genomes.
Fong JH; Murphy TD; Pruitt KD
BMC Genomics; 2013 Sep; 14():654. PubMed ID: 24063302
[TBL] [Abstract][Full Text] [Related]
14. Gene calling and bacterial genome annotation with BG7.
Tobes R; Pareja-Tobes P; Manrique M; Pareja-Tobes E; Kovach E; Alekhin A; Pareja E
Methods Mol Biol; 2015; 1231():177-89. PubMed ID: 25343866
[TBL] [Abstract][Full Text] [Related]
15. Assessing the impact of human genome annotation choice on RNA-seq expression estimates.
Wu PY; Phan JH; Wang MD
BMC Bioinformatics; 2013; 14 Suppl 11(Suppl 11):S8. PubMed ID: 24564364
[TBL] [Abstract][Full Text] [Related]
16. Using multiple reference genomes to identify and resolve annotation inconsistencies.
Monnahan PJ; Michno JM; O'Connor C; Brohammer AB; Springer NM; McGaugh SE; Hirsch CN
BMC Genomics; 2020 Apr; 21(1):281. PubMed ID: 32264824
[TBL] [Abstract][Full Text] [Related]
17. Rascaf: Improving Genome Assembly with RNA Sequencing Data.
Song L; Shankar DS; Florea L
Plant Genome; 2016 Nov; 9(3):. PubMed ID: 27902792
[TBL] [Abstract][Full Text] [Related]
18. A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals.
Chen J; Rozowsky J; Galeev TR; Harmanci A; Kitchen R; Bedford J; Abyzov A; Kong Y; Regan L; Gerstein M
Nat Commun; 2016 Apr; 7():11101. PubMed ID: 27089393
[TBL] [Abstract][Full Text] [Related]
19. Plant genome and transcriptome annotations: from misconceptions to simple solutions.
Bolger ME; Arsova B; Usadel B
Brief Bioinform; 2018 May; 19(3):437-449. PubMed ID: 28062412
[TBL] [Abstract][Full Text] [Related]
20. AGOUTI: improving genome assembly and annotation using transcriptome data.
Zhang SV; Zhuo L; Hahn MW
Gigascience; 2016 Jul; 5(1):31. PubMed ID: 27435057
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
