2015年2月19日 · By definition, the promoter of any transcribed sequence is immediately surrounding the annotated or experimentally defined (by 5' RACE) 5' end of the gene. This can be viewed best with some...

PhagePromoter - is a tool for locating promoters in phage genomes, using machine learning methods. This is the first online tool for predicting promoters that uses phage promoter data and the first to identify both host and phage promoters with different motifs. It is part of Galaxy.

2015年10月14日 · How to find and retrieve promoter sequences from genome databases. Promoter sequences are usually the sequence immediately upstream the transcription start site (TSS) or first exon. If we know the TSS of a gene, we will know with confidence where the promoter is even without experimental characterization.

The sequence from beginning to the first capital letter is the promoter sequence. Click Scan, type the promoter sequence (FASTA type) into this region. For example PLD1 promoter sequence, Click “scan”; Click “CSV” to download results, choose the possible binding sites according score.

2014年12月30日 · How you can get that sequence is: If you know the gene coordinates (or annotated gene coordinates if the gene is not characterized) of your gene of interest in a particular chromosome then...

2017年2月2日 · To fetch the upstream sequence for a specific gene, use the Table Browser. Enter the genome, assembly, and select the knownGene table. Paste the gene name or accession number in the identifier...

The Gene Sorter offers two options for displaying and downloading sequence associated with the genes in the table. Clicking on the sequence button will fetch associated protein, mRNA, promoter, or genomic sequence.

Therefore, the distribution of histone modifications can be analyzed by ChIP-seq to find the promoter and enhancer regions of genes and whether they activate or repress gene expression. Five core histone modifications are widely used for ChIP-seq analysis:

The promoter region is one of the key controllers for initiating transcription leading to gene regulation, even when the binding motif is known for a given TF loci with that motif may or may not be relevant in regulation. In a promoter containing motif, cell-type-specific or environmental cues affect accessibility.

This chapter describes the advanced approaches to identify promoters in animal, plant and bacterial sequences. Also, we discuss an approach to identify statistically significant regulatory motifs in genomic sequences. Promoter sequences …