Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Blast organism mask susanklein Bioinformatics 19 12-19-2017 07:22 AM
ChIP-seq of conventional TFs: what are the peaks w/o the motif? apredeus Bioinformatics 3 04-14-2014 08:48 AM
Subject organism name from Blastp result dgio Bioinformatics 1 10-29-2012 04:18 AM
Which organism has the best GO annotations? RNAddict Bioinformatics 8 08-21-2012 06:51 AM
list of organism with unknown sequence ranjani Bioinformatics 1 07-13-2012 06:01 AM

Thread Tools
Old 01-20-2015, 05:57 AM   #1
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?
Fernas is offline   Reply With Quote
Old 01-23-2015, 01:17 PM   #2
Senior Member
Location: Switzerland

Join Date: Aug 2008
Posts: 124

I'll either search against a TF database such as DBD/Pfam or blast the proteins to known TFs.
Melissa is offline   Reply With Quote

denovo assembly, transcription factor

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 03:49 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO