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Genome Annotation and Assembly

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...

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Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

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ESTpass: a web-based server for processing and annotating expressed sequence tag (EST) sequences.

Byungwook Lee¹, Taehui Hong, Sang Jin Byun

¹Korean BioInformation Center, KRIBB, Daejeon 305-817, Korea.

Nucleic Acids Research

|May 29, 2007

Summary

ESTpass is a web server that processes and annotates expressed sequence tag (EST) data. It offers integrated sequence cleansing, assembly, and comprehensive annotation for improved gene discovery.

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Expressed Sequence Tag (EST) projects generate vast amounts of sequence data.
Efficient processing and annotation of ESTs are crucial for gene discovery and functional genomics.

Purpose of the Study:

To develop ESTpass, a web-based server for comprehensive processing and annotation of EST data.
To provide an integrated pipeline for EST sequence cleansing, assembly, and functional annotation.

Main Methods:

ESTpass accepts FASTA-formatted EST files and quality files.
It employs a pipeline including sequence cleansing, d2_cluster and CAP3 for assembly, and chimeric EST detection.
Annotation is performed using RefSeq, InterPro, GO, and KEGG databases.

Main Results:

ESTpass successfully processes and annotates EST sequences, producing putative transcripts.
The server integrates cleansing and annotation, with rigorous chimeric EST detection.
Results are delivered via email and accessible through a web browser with summary, cleansing, and annotation reports.

Conclusions:

ESTpass offers an integrated and user-friendly solution for EST data analysis.
The server facilitates efficient gene discovery through robust processing and exhaustive annotation.
ESTpass enhances the utility of EST data for biological research.