scholarly journals The vertebrate genome annotation (Vega) database

2007 ◽  
Vol 36 (Database) ◽  
pp. D753-D760 ◽  
Author(s):  
L. G. Wilming ◽  
J. G. R. Gilbert ◽  
K. Howe ◽  
S. Trevanion ◽  
T. Hubbard ◽  
...  
Keyword(s):  
Genome Annotation ◽  
Vertebrate Genome

scholarly journals The Vertebrate Genome Annotation (Vega) database

2004 ◽  
Vol 33 (Database issue) ◽  
pp. D459-D465 ◽  
Author(s):  
J. L. Ashurst
Keyword(s):  
Genome Annotation ◽  
Vertebrate Genome

scholarly journals The Vertebrate Genome Annotation browser 10 years on

2013 ◽  
Vol 42 (D1) ◽  
pp. D771-D779 ◽  
Author(s):  
Jennifer L. Harrow ◽  
Charles A. Steward ◽  
Adam Frankish ◽  
James G. Gilbert ◽  
Jose M. Gonzalez ◽  
...  
Keyword(s):  
Genome Annotation ◽  
Vertebrate Genome

scholarly journals The importance of identifying alternative splicing in vertebrate genome annotation

Database ◽  
2012 ◽  
Vol 2012 ◽  
Author(s):  
Adam Frankish ◽  
Jonathan M. Mudge ◽  
Mark Thomas ◽  
Jennifer Harrow
Keyword(s):  
Alternative Splicing ◽  
Genome Annotation ◽  
Vertebrate Genome

Phylogenetic Analysis of T-Box Genes Demonstrates the Importance of Amphioxus for Understanding Evolution of the Vertebrate Genome

Genetics ◽  
2000 ◽  
Vol 156 (3) ◽  
pp. 1249-1257
Author(s):  
Ilya Ruvinsky ◽  
Lee M Silver ◽  
Jeremy J Gibson-Brown
Keyword(s):  
Phylogenetic Analysis ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Gene Families ◽  
Vertebrate Evolution ◽  
Whole Genome ◽  
Vertebrate Genome ◽  
T Box ◽  
Genetic Complexity ◽  
History Of

Abstract The duplication of preexisting genes has played a major role in evolution. To understand the evolution of genetic complexity it is important to reconstruct the phylogenetic history of the genome. A widely held view suggests that the vertebrate genome evolved via two successive rounds of whole-genome duplication. To test this model we have isolated seven new T-box genes from the primitive chordate amphioxus. We find that each amphioxus gene generally corresponds to two or three vertebrate counterparts. A phylogenetic analysis of these genes supports the idea that a single whole-genome duplication took place early in vertebrate evolution, but cannot exclude the possibility that a second duplication later took place. The origin of additional paralogs evident in this and other gene families could be the result of subsequent, smaller-scale chromosomal duplications. Our findings highlight the importance of amphioxus as a key organism for understanding evolution of the vertebrate genome.

scholarly journals Uncovering transcriptional dark matter via gene annotation independent single-cell RNA sequencing analysis

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Michael F. Z. Wang ◽  
Madhav Mantri ◽  
Shao-Pei Chou ◽  
Gaetano J. Scuderi ◽  
David W. McKellar ◽  
...  
Keyword(s):  
Single Cell ◽  
Genome Annotation ◽  
Gene Annotation ◽  
Active Regions ◽  
Sequencing Analysis ◽  
Biologically Relevant ◽  
Mole Rat ◽  
Genome Annotations ◽  
Cell Expression ◽  
High Quality Genome

AbstractConventional scRNA-seq expression analyses rely on the availability of a high quality genome annotation. Yet, as we show here with scRNA-seq experiments and analyses spanning human, mouse, chicken, mole rat, lemur and sea urchin, genome annotations are often incomplete, in particular for organisms that are not routinely studied. To overcome this hurdle, we created a scRNA-seq analysis routine that recovers biologically relevant transcriptional activity beyond the scope of the best available genome annotation by performing scRNA-seq analysis on any region in the genome for which transcriptional products are detected. Our tool generates a single-cell expression matrix for all transcriptionally active regions (TARs), performs single-cell TAR expression analysis to identify biologically significant TARs, and then annotates TARs using gene homology analysis. This procedure uses single-cell expression analyses as a filter to direct annotation efforts to biologically significant transcripts and thereby uncovers biology to which scRNA-seq would otherwise be in the dark.

Whole genome sequencing and genome annotation of Dermacoccus abyssi strain HZAU 226 isolated from spoiled eggs

Genomics ◽  
2020 ◽  
Author(s):  
Xinshuai Zhang ◽  
Yao Ruan ◽  
Wukang Liu ◽  
Qian Chen ◽  
Lihong Gu ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genome Annotation ◽  
Whole Genome
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