Get DNA Binding Domains of Transcription Factors

[Fernas]

My question is basic and as follows:

I have 1000 transcription factors (TFs) which I have retrieved their amino acid sequences from Uniprot. I want to extract the DNA binding domain(s) for each of them (start positin, end position..etc). How can I do that?

I heard of pfam but I am wondering if I need to submit each of the TFs or there is an automatic way to submit all of them and parse outputs? any other tools that give me more options?

[WhatsOEver]

You can use the PfamScan perl script with which you can do batch domain annotation on your PC (see here: ftp://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/). In the output you will have start and end positions of each domain it identifies.

[Fernas]

Many thanks @WhatsOEver.
I am still wondering if pfam is enough. I just found (interproScan) tool which searches other databases in addition to pfam (e.g. BlastProDom,FPrintScan, HMMPIR, ProfileScan..etc). I am wondering if this is a good option or it will create redundant and/or less accurate outputs?

[WhatsOEver]

Well, there are always a couple of tools which will basically do the same but this a little different

I prefer PfamScan as the database is well curated and the output easy to handle.
The problem with tools like interpro (in my opinion) is that they may use older versions of the tools from which they collect the prediction (signalp 3 instead of 4 was for example used for some time).

If you are not sure which motif prediction tool to use or which are available at all, you may find the following link useful: http://molbiol-tools.ca/Motifs.htm

[Fernas]

Thank you very much @WhatsOEver. That was of great help!