GASS: genome structural annotation for Eukaryotes based on species similarity

BMC Genomics
Ying WangXiaoye Lei

Abstract

With the development of high-throughput sequencing techniques, more and more genomes were sequenced and assembled. However, annotating a genome's structure rapidly and expressly remains challenging. Current eukaryotic genome annotations require various, abundant supporting data, such as: species-specific and cross-species protein sequences, ESTs, cDNA and RNA-Seq data. Collecting those data and merging their analytical results to achieve a consistent complete annotation is a complex, time and cost consuming task. In our study, we proposed a fast and easy-to-use computational tool: GASS (Genome Annotation based on Species Similarity). It annotates a eukaryotic genome based on only the annotations from another similar species. With aligning the exons' sequences of an annotated similar species to the un-annotated genome, GASS detects the optimal transcript annotations with a shortest-path model. In our study, GASS was used to achieve the rhesus annotations based on the human annotations. The produced annotations were evaluated by comparing them to the two existing rhesus annotation databases (RefSeq and Ensembl) directly and being aligned with three RNA-Seq data of rhesus. The experiment results showed that more than 65% RefSeq ex...Continue Reading

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Citations

Aug 20, 2020·PloS One·Dina A El-KhishinMohamed I Abouelhoda
Nov 13, 2020·PLoS Computational Biology·Hyungtaek JungSeong-Il Eyun

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Datasets Mentioned

BETA
SRR594464

Methods Mentioned

BETA
RNA-Seq
DNA-Seq

Software Mentioned

SOAPdenovo
BLAST
ABySS
Align
Ensembl
GENCODE
Trinity
rheMac2
RefSeq
Basic Local Alignment Search Tool ( BLAST )

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