User Tools

Site Tools


This is an old revision of the document!

A PCRE internal error occured. This might be caused by a faulty plugin

====Genome Annotation with RAST and Artemis==== ===Presented by Jeff Long=== The RAST server: Rapid Annotations using Subsystems Technology - Takes a genome and annotates them. - When you enter the website, you can upload a genome and annotate it. - Takes some time to run: 1-2 weeks for a small genome (6-8mb). - The SEED Viewer is an annotation tool which gives you a pie chart for all the subsystems for all genes found. - Jeff showed a slide on //Calothrix//, a nitrogen fixing organism found in the ocean. - Clicking on a subsystem (biosynthesis pathway) would take you to a list of genes found within your organism. - Genes found in the subsystem can be further evaluated in a detailed page. - The data format is analgous to the UCSC genome browser. - Shows you genes with similar DNA Assembly of the genome of //Calothorix rhizosoleniae// strain sc01, a marine nitrogen fixing cyanobacterium. Nitrogen Fixation - Take N2 gas and convert it into a bioavailabe form of nitrogen. - In the open ocean, there is a dearth of usable nitrogen. - //Calothorix// has a string of heterocysts (nitrogen-fixing cells) and vegetative cells (oxygen utilizing cells) Artemis Comparison tool (ACT) - Java-based programs that can be run from a browser. - Artemis - Overview window that is similar to the UCSC genome browser - DNA view window shows the actual sequence. - Feature table - Shows information in embl format - DNA Plotter - Shows sequence plotted onto a circle-- Similar to CircOS program used by David Bernick. - WebACT - With closely related genomes, program draws the syntany between them. - Gives an instantaneous view of the similarity between two genomes. - Maps which portions of genome map to another genome. - BamView - No details on this tool, but it comes packaged with ACT.

You could leave a comment if you were logged in.
lecture_notes/05-17-2010.1274141676.txt.gz · Last modified: 2010/05/18 00:14 by learithe