deletions | additions       diff --git a/Genome Assembly and Annotation.md b/Genome Assembly and Annotation.md  index 9d8c4e5..898440c 100644  --- a/Genome Assembly and Annotation.md  +++ b/Genome Assembly and Annotation.md 
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Hover over the "Your Jobs" tab at the top of the page and click on "Upload New Job." In order to proceed you must specify a domain, a genus, a species, and the genetic code (usually "11".) Click "Finish the Upload."  The annotation will take some time, ranging from 2 hours to a few days, depending on server load. RAST will email you when it is complete. Once the annotation is complete, use their SEED Viewer to explore the annotation and metabolic pathways of the organism. From the RAST results, you can obtain information such as the presence or absence of a particular gene/pathway and you can compare the annotation to other genomes in their database.  ###Obtain the Full-Length 16S Sequence from the Assembly    (Skip this step if you are building the tree using the 16S sequence from Sanger sequencing)  1. Go to RAST and sign in  2. On the “Jobs Overview" page, click on view details (under annotation progress) for the microbe you are working with.  3. Click on Browse annotated genome in SEED viewer (At the top of the page)  4. Click on Browse through the features of [organism name]  5. Under Function search for “ssurna” or “SSU rRNA”  (if it doesn't work at first then refresh the page)  6. Find the ssuRNA that is 1400-1800 bp in length (often Illumina assemblies also have fragments of 16S sequence that are only a few hundred bp long)  7. Click on the Feature ID for that sequence  8. Click on the Sequences tab (around the middle of the page )  9. Click on Show Fasta  9. Click on Download Sequences and save as a fasta file. Rename the file to something useful.  11. Double check the identity of the sequence at BLAST:  [http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome](http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome)