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Old 02-21-2013, 07:01 AM   #1
Sepalous
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Location: Cardiff

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Default Annotation help

Hi,

This may be a series of extremely basic questions, but I’ve only had a little bioinformatics training. I am quickly running out of time for a report where I’m required to annotate a genome using any means at my disposal. I was just hoping for a little guidance on the process of annotation…

I’ve managed to do the 16s rRNA analysis of closest ancestors, as well as the analysis of metabolic pathways that were generated by RAST and Asgard. Where I’m having trouble is getting an annotation on to Artemis, the output of RAST doesn’t seem to want to load and I kept getting the error message: while reading from HW RAST.gbk: source can't have >NODE_3_length_185_cov_148.318924 as a qualifier. I tried to fix this using Jemboss and Union, but it didn’t carry the details of the genes across to Artemis. Has anybody got any ideas how to fix this? I've shared the file here if you want a gander. https://www.dropbox.com/sh/wjrzmr6p0auvcox/1Nq2BFKOXN

Also, how would I go about characterising the operons? I’ve tried looking for operon predication software, but they seem to be above my competency level and I can’t get the to work. Are there any online suites which would do the same job, or could recommend a newbie-friendly method?

Thanks, Sepalous
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Old 02-21-2013, 12:46 PM   #2
CharlieB
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Location: Regina, Saskatchewan, Canada

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Default

We're all in over heads with this work, But you gotta start somewhere. Don't let other people's apparent expertise or gobbledeegoop dissuade or intimidate you. We're all newbies now. Just focus on what you know, what you understand, the thread of inquiry this allows. Nobody knows the entire realm these days. Do your best to communicate in simple everyday language or long established scientific language.
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