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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.

Tutorial and training materials by OpenHelix

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.

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You'll learn:

  • Browse and search through the available archaeal genome data to find what you need
  • Understand the data you obtain and link to more information
  • Customize and manipulate your data in the genome browser
  • Use Blat and the In-Silico PCR tools to search by sequence
  • Understand and access some of the additional advanced tools available


Related tutorials

This tutorial is a part of the tutorial group UCSC Tutorials. You might find the other tutorials in the group interesting:

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Recent BioMed Central research articles citing this resource

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

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

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

Rouchka C Eric et al., Proceedings of the Eleventh Annual UT-ORNL-KBRIN Bioinformatics Summit 2012 UT-ORNL-KBRIN Bioinformatics Summit 2012 11th Annual UT-ORNL-KBRIN Bioinformatics Summit 2012. BMC Bioinformatics (2012) doi:10.1186/1471-2105-13-S12-A1

More about the resource:

The UCSC Archaeal Genome Browser was developed from the UCSC Genome Browser, originally devoted to human data. The group at UCSC has tailored this browser to the needs of the archaeal research community, while still retaining the extensive features and options the original browser provided. The UCSC Archaeal Genome Browser provides you with both basic and advanced methods to search, browse and manipulate any genomic regions of interest in many archaeal species.


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The materials and slides offered can not be resold or used for profit purposes. Reproduction, distribution and/or use is strictly limited to instructional purposes only and can not be used for for monetary gain or wide distribution.
Copyright 2009, OpenHelix, LLC.

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