Mitochondrial and Chloroplast DNA in Scaffolds. Goal Determine which scaffolds have mitochondrial or chloroplast DNA – Grape and Arabidopsis reference.

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Mitochondrial and Chloroplast DNA in Scaffolds

Goal Determine which scaffolds have mitochondrial or chloroplast DNA – Grape and Arabidopsis reference sets Ideally somehow annotate scaffolds/Contigs

Process A lot of blast results Program – Splits up blast results – Counts the number of times a specific scaffold appears Store data in format that is editable in excel

454

Illumina

Why I used the Top Most Frequent hits

What Next? Possible additional feature is to pull out scaffolding sequences that give x hits Annotation issues with geneious

What we can do in Geneious Scaffolds identified through blast and counting hits re-Blasted as queries against grape and Arabidopsis mitochondria DNA – Just took one of the scaffolds with the most hits and re-blasted Some alignment with ORFs

1 scaffold against all mitochondrial genes for grape and Arabidopsis Notice 14 total hits… Different e-value? Program wrong?

Mitochondial Gene Scaffold/contig

How Accurate is Geneious ORF?

Questions… How do we want to use geneious? Is further work really helpful? Or good enough know these scaffolds as flagged?