The publicly available UCSC Archaeal Genome Browser provides you with many research and analysis tools that can be used to examine the genomes of more than 50 microbial species from the domain archaea. It is based on the USCS Genome Browser, and thus contains many of the easy to use features that some of you have already become familiar with. Data also include the genomes of important bacteria for comparison.
Searching and browsing through the genomic data is convenient and simple. There are a variety of basic and advanced tools, as well. You can search by DNA or protein sequence using BLAT, or use the UCSC In-Silico PCR tool to search by primer sequences, and then examine your predicted PCR product. The Table Browser enables you to retrieve the data from the data tracks you want in text format. And it is very easy to download and format any sequence you want using the "Get DNA in Window" feature offered. Multiple options and methods enable you to customize your data display to your liking. The UCSC Archaeal Genome Browser is a valuable resource to anyone interested in archaeal genome research.
You will learn:
This tutorial is a part of the tutorial group UCSC Tutorials. You might find the other tutorials in the group interesting:
ENCODE Foundations: ENCyclopedia of DNA Elements
UCSC Genome Browser: The Additional Tools: Additional tools at the UCSC Genome Browser
UCSC Genome Browser: Custom Tracks and Table Browser: UCSC Genome Browser advanced topics
ENCODE Data at UCSC: ENCODE Data at UCSC
UCSC Genome Browser: An Introduction: The UCSC Genome Browser Introduction
This tutorial is a part of the tutorial group Microbe resources. You might find the other tutorials in the group interesting:
Viral Genomes at NCBI: Viral genome resources including single-stranded or double-stranded RNA or DNA viruses
CMR: Comprehensive Microbial Resource
Integrated Microbial Genomes (IMG): IMG is a powerful community resource for the comparative analysis and annotation of microbial genome data.
Complete Microbial Genomes: An extensive collection of data, resources and tools for prokaryotic genomic analysis
Integrated Microbial Genomes with Microbiome samples (IMG/M): IMG/M provides tools for analyzing the functional capability of microbial communities based on their metagenome sequence
VBRC: The Viral Bioinformatics Resource Center
GenoCAD: Computer-Assisted Design software for synthetic biology
GenoCAD Advanced Topics: Computer-Assisted Design software for synthetic biology
Genome Databases (prok + viral) : Genomic databases or repositories primarily aimed at prokaryotic or viral organisms. Some may contain eukaryotic data as well.
NAR database issue (always a treasure trove): The advance access release of most of the NAR database issue articles is out. As usual, this this database issue includes a wealth of new and updated data repositories and analysis tools. We'll be wri...
Tip of the Week: Comparing Microbial Databases: A few weeks ago a commenter asked me to compare IMG (Integrated Microbial Genomes) to the UCSC Microbial Genome browser. I've been exploring & thinking since then & am going to give a very brief compa...
We are in Singapore (GGID): OpenHelix (and by "OpenHelix" I mean "I" :) is in Singapore this week for the Genetics and Genomics of Infectious Disease conference sponsored by Nature Publishing Group, American Society of Human Gene...
Recent BioMed Central research articles citing this resource
Kiljunen Saija et al., Generation of comprehensive transposon insertion mutant library for the model archaeon, Haloferax volcanii , and its use for gene discovery. BMC Biology (2014) doi:10.1186/s12915-014-0103-3
Nguyen-Duc Trong et al., The genome-wide binding profile of the Sulfolobus solfataricus transcription factor Ss-LrpB shows binding events beyond direct transcription regulation Prokaryote microbial genomics. BMC Genomics (2013) doi:10.1186/1471-2164-14-828
Lin Yu-fei et al., A combination of improved differential and global RNA-seq reveals pervasive transcription initiation and events in all stages of the life-cycle of functional RNAs in Propionibacterium acnes , a major contributor to wide-spread human disease Prokaryote microbial genomics. BMC Genomics (2013) doi:10.1186/1471-2164-14-620
Nalabothula Narasimharao et al., Archaeal nucleosome positioning in vivo and in vitro is directed by primary sequence motifs Comparative and evolutionary genomics. BMC Genomics (2013) doi:10.1186/1471-2164-14-391
Bernhardt S Harold et al., Primordial soup or vinaigrette: did the RNA world evolve at acidic pH?. Biology Direct (2012) doi:10.1186/1745-6150-7-4