Question: Download transfac public database
1
gravatar for bharata1803
3.2 years ago by
bharata1803420
Japan
bharata1803420 wrote:

I downloaded transfac PWM data from this link. From the date, those data is really old, from 1997 and the transfac version is 3.7. Is there any newer transfac downloadable matrix data? I check the current transfac version is 8.3. I know transfac free data is limited and to get full data I need to pay for it. Currently, I'm okay using the free data but I need the matrix file in a way I can processed automatically (in txt format or any other text format). Other tools that use transfac data is PROMO but I can not download the matrix. Is there any suggestion? Thank you very much.

ADD COMMENTlink modified 3.2 years ago by UnivStudent380 • written 3.2 years ago by bharata1803420
3
gravatar for UnivStudent
3.2 years ago by
UnivStudent380
Canada
UnivStudent380 wrote:

You can download the Transfac public matrices and much more in the CIS-BP database. Just select Transfac from the evidence type dropdown.

ADD COMMENTlink written 3.2 years ago by UnivStudent380
0
gravatar for natasha.sernova
3.2 years ago by
natasha.sernova3.5k
natasha.sernova3.5k wrote:

Why don't you see any matrices going to

"Other tools:

ViewMatrices:view details on weight matrices being used" on PROMO-page?

Or when you press on the link VIEW MATRICES in the left column?

on the same PROMO-page?

ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by natasha.sernova3.5k

Yes, I have tried that but it gives me web page result. Do you know how to download the file? Or I must parse the data from html file?

ADD REPLYlink written 3.2 years ago by bharata1803420

It has given this page to me:

http://alggen.lsi.upc.es/cgi-bin/promo_v3/promo/promoinit.cgi?dirDB=TF_8.3

SelectSpecies SelectFactors ViewMatrices SearchSites MultiSearchSites

I selected ViewMatrices

I saw the list of them on the right side, selected any random line and got this:

Antp [T00026]

Matrix and consensus sequence:

A

C

G

T

0 9 9 0 3 2

0 0 0 0 0 0

0 0 0 0 3 5

9 0 0 9 3 2

T A A T A G

But this is to rewrite it by hands, that's not OK.

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by natasha.sernova3.5k

These old posts may help as well:

Best Database Of Transcription Factor Binding Sites

See this paper, it may help.

http://nar.oxfordjournals.org/content/44/D1/D144.full.pdf+html

as well as this site:

http://www.biobase-international.com/product/transcription-factor-binding-sites from 2015

also this database from 2010:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2841680/

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by natasha.sernova3.5k

Thank you very much.

ADD REPLYlink written 3.2 years ago by bharata1803420

I'm sorry but I have another question. From the method that you've shown me to get matrix from PROMO, is it only for human or for all species? I notice in other function, PROMO has species filter but when I click the other tools -> ViewMatrices, I only need to choose transcription factor names. I have successfully get that data but wondering about the species. Thank you very much.

ADD REPLYlink written 3.2 years ago by bharata1803420

See this paper:

http://nar.oxfordjournals.org.sci-hub.cc/content/31/13/3651.short

At least 4 species: humans, mouse, chicken and frog.

I will try to find a full version.

"PROMO ‘ MultiSearchSites ’ output example. The example corre- sponds to the regulatory region of the cardiac alpha-actin gene from four differ- ent vertebrate species: humans, mouse, chicken and frog. Only those binding site predictions that appear in all four sequences are shown, as boxes of different col- our and number. The image below, where the sequences are shown, is the result of selecting ‘ Zoom ’ in the main results page above. The image on the right is a detail of the SRF (serum response factor) — binding site predictions on the sequences. It also shows the weight matrix for the SRF recognition site and ran- dom expectation (RE) values for different levels of sequence-matrix similarity. The RE is calculated with a model that considers that all nucleotides are equally probable and also with a model that considers the nucleotide composition in the query sequence (in the picture represented by blue bars below matrix)."

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by natasha.sernova3.5k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 619 users visited in the last hour