Improving Silkworm Genome Annotation Using a Proteogenomics Approach

2019 ◽  
Vol 18 (8) ◽  
pp. 3009-3019 ◽  
Author(s):  
Xiaogang Ye ◽  
Xiaoli Tang ◽  
Xiaoxiao Wang ◽  
Jiaqian Che ◽  
Meiyu Wu ◽  
...  
Keyword(s):  
Genome Annotation ◽  
Silkworm 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

scholarly journals Genome annotation by high-throughput 5' RNA end determination

2004 ◽  
Vol 101 (6) ◽  
pp. 1650-1655 ◽  
Author(s):  
B. J. Hwang ◽  
H.-M. Muller ◽  
P. W. Sternberg
Keyword(s):  
High Throughput ◽  
Genome Annotation

scholarly journals MADAP, a flexible clustering tool for the interpretation of one-dimensional genome annotation data

2007 ◽  
Vol 35 (Web Server) ◽  
pp. W201-W205 ◽  
Author(s):  
C. D. Schmid ◽  
T. Sengstag ◽  
P. Bucher ◽  
M. Delorenzi
Keyword(s):  
Genome Annotation ◽  
One Dimensional ◽  
Annotation Data

scholarly journals The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)

2015 ◽  
Vol 10 (1) ◽  
Author(s):  
Marcel Huntemann ◽  
Natalia N. Ivanova ◽  
Konstantinos Mavromatis ◽  
H. James Tripp ◽  
David Paez-Espino ◽  
...  
Keyword(s):  
Operating Procedure ◽  
Genome Annotation ◽  
Standard Operating Procedure ◽  
Microbial Genome ◽  
Annotation Pipeline ◽  
Standard Operating

scholarly journals The 2008 update of the Aspergillus nidulans genome annotation: A community effort

2009 ◽  
Vol 46 (1) ◽  
pp. S2-S13 ◽  
Author(s):  
Jennifer Russo Wortman ◽  
Jane Mabey Gilsenan ◽  
Vinita Joardar ◽  
Jennifer Deegan ◽  
John Clutterbuck ◽  
...  
Keyword(s):  
Aspergillus Nidulans ◽  
Genome Annotation ◽  
Community Effort

scholarly journals ECgene: genome annotation for alternative splicing

2004 ◽  
Vol 33 (Database issue) ◽  
pp. D75-D79 ◽  
Author(s):  
P. Kim
Keyword(s):  
Alternative Splicing ◽  
Genome Annotation

scholarly journals Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam

2014 ◽  
Vol 14 (1) ◽  
Author(s):  
Juanjuan Chai ◽  
Guruprasad Kora ◽  
Tae-Hyuk Ahn ◽  
Doug Hyatt ◽  
Chongle Pan
Keyword(s):  
Genome Annotation
Sign in / Sign up

Export Citation Format

Share Document