PROMO (prediction of transcription factor binding sites), ESSEM ...

PROMO is a program to predict transcription factor binding sites in DNA sequences. It can analyse one sequence or multiple related sequences. PROMO (prediction of transcription …

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FAQs about PROMO (prediction of transcription factor binding sites), ESSEM ... Coupon?

What is TFBS recognition?

The recognition of transcription factor binding sites (TFBSs) is the first step on the way to deciphering the DNA regulatory code. A large variety of computational approaches and corresponding in silico tools for TFBS recognition are available, each having their own advantages and shortcomings. ...

What is TFBS based search?

TFBS, transcription factor binding site. The most popular approach for TFBS prediction, PWM-based search, considers that the nucleotides of each position exhibit independent participation in the DNA-protein interactions. ...

Which TFBS can be accommodated by tffms?

Another feature of the TFBSs that can be accommodated by TFFMs is flexible length. A subset of TFs bind to the DNA with different structural conformations, leading to TFBSs of different lengths – . In order to model a binding site with a flexible length, we can use the transition probabilities of the underlying HMMs of the TFFMs. ...

Are TFFm models suitable for TFBS prediction?

In applications, the TFFM models have been shown to handle variable spacing between half sites, and to allow for the incorporation of flanking sequence properties into TFBS analysis. With a convenient software package and a breadth of opportunities for improvement, TFFMs are a suitable foundation for the next generation of TFBS prediction. ...

Why do TFBS predictions need to be more reliable?

As mentioned previously, because gene regulation is affected by various factors (e.g. organs, developmental stages and surrounding environments), not only genetic information (DNA sequence) but also epigenetic status, such as histone marks and DNA methylation (i.e. chromatin state), need to be considered for more reliable TFBS predictions. ...

What is tfbspred TFBS prediction?

TFBSPred TFBS prediction is based on TFFM searches which are executed in the webtool backend, after the users have submitted their data. To this end, the TFFM framework (22), as well as its prerequisites, the general hidden Markov model (GHMM) (42) and Biopython (43) libraries, were installed. ...