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Old 01-20-2015, 05:57 AM   #1
Fernas
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Location: Middle East

Join Date: Apr 2013
Posts: 74
Default Identify TFs in New Assembled Organism

A denovo assembly of a new organism that lives in the sea (from the animal kingdom but we do not know its type specifically) have been prepared.

We want now to identify all possible transcription factors in this genome. So, I was thinking in the following steps:

1) Send the translated sequences (amino acid sequences of the genome) to Blast to identify gene/protein locations/sequences in the genome
2) Prepare list of TFs from multiple sources for different organisms (e.g. all TF Sequences of TFs in TRANSFAC, Human TFs...etc)
3) Use ORTHOMCL to identify which of TFs in step 2 is close (in the same cluster) to my proteins that were identified in step 1.

What do you think? is there any other suggestions?
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Old 01-23-2015, 01:17 PM   #2
Melissa
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I'll either search against a TF database such as DBD/Pfam or blast the proteins to known TFs.
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