Question

Busco lineage database for Staphylococcus pasteuri assembly

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5.5 years ago

jeetsahu ▴ 10

I am doing assessment of assembly of Staphylococcus pasteuri genome for the orthologue presence absence using blastn with BUSCO. Which lineage database to use for the same?

gene Assembly genome busco • 1.9k views

ADD COMMENT • link updated 5.5 years ago by WouterDeCoster 47k • written 5.5 years ago by jeetsahu ▴ 10

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This is a question, not a forum post. Please use a more informative title, for example in this case mentioning BUSCO. In addition, please use sensible tags. As such experts can easily find your question. I have changed this for you now, but keep this in mind for further questions.

ADD REPLY • link 5.5 years ago by WouterDeCoster 47k

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Thanks! will keep this mind.

ADD REPLY • link 5.5 years ago by jeetsahu ▴ 10

score 2 · Accepted Answer · 2018-10-30

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5.5 years ago

GenoMax 141k

Bacillales would be relevant (download link from Busco site).

ADD COMMENT • link 5.5 years ago by GenoMax 141k

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What should be the "model" organism to use in augustus for gene prediction?

ADD REPLY • link 5.5 years ago by jeetsahu ▴ 10

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Why do you want to use Augustus for a bacterial genome. AUGUSTUS is a program that predicts genes in **eukaryotic** genomic sequences.

You may want to use prokka instead (https://github.com/tseemann/prokka ).

ADD REPLY • link 5.5 years ago by GenoMax 141k

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Thanks for correction. Does prokka also use some model organism for gene prediction ?

ADD REPLY • link 5.5 years ago by jeetsahu ▴ 10