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Old 06-21-2012, 01:03 AM   #1
zinky
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Location: china

Join Date: Dec 2011
Posts: 48
Question de novo assembling sequences to do go or pathway analysis

hi! here is my problem: i have some sequence assembled by trinity ,with raw data and downstream Trinity scripts ,a list of Differencial Expression seqs were collected. i wanna do GO and Kegg analysis with those sequences and i have no idea on how to do it cause there is no reference genome .so can anyone give me some advice or recommand some software to do this? thanks!
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Old 09-28-2012, 02:51 AM   #2
Anemone
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Location: Norway

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Default De novo sequence analyses

Hi! I am using Blast2GO (http://blast2go.com/b2ghome) for my de novo analyses. You just have to upload your sequences in a fasta format and first blast them against the online database before getting any GO terms for your sequences. You can also get the information in which pathways your annotated genes are represented through KEGG. I hope that helps!! I do not know yet about any other programme, which can do GO and KEGG for de novo analyses.
Good luck!
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