PORTOs - Promoter Retrieval Tool
Idea: A web-based tool for easy retrieval and sensitive analysis of promoter regions of genes from various organisms
Problem:
- getting the promoter region of genes - even if annotated correctly - is tedious and time-consuming.
- analyzing co-regulated/orthologous promoters for common regulatory regions with high sensitivity is not automated.
Solution: mine the NCBI resource for promoter regions of genes
- by entering an NCBI RefSeq accession number (protein, mRNA), PORTOs retrieves the fasta-formatted region upstream of the gene with a variable length.
- by performing BLAST-searches in combination with a SPIDEY alignment (NCBI) of the best hits, PORTOs is able to retrieve sequences of genes that are a) not correctly predicted or b) not predicted at all.
- by BLAST2 searches of orthologuous/co-regulated genes, find common regions with high sensitivity.
- pattern-searches using consensus sequences find corresponding transcription factor binding sites.
Input:
- an NCBI RefSeq accession number
- the desired length of the promoter fragment
- the mRNA accession number + the species, in case the gene is not correctly predicted or not predicted at all
- transcription factor consensus motif
Enter either a single accession number or a multiple fasta-file containing co-regulated or orthologous genes. PORTOs will find orthologues by searching through the HomoloGENE database or performing BLAST and SPIDEY searches. After retrieval of promoters, BLAST-2-SEQ runs are performed for each sequence pair to find overlapping regions. Transcription factor binding sites are searches by simple pattern searches. The output is generated, annotated and shown to the user.