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PromoSer - overview

Researchers studying the mechanisms of transcription regulation are commonly interested in the proximal promoter regions of genes. Often one wants to obtain these regions for a large number of related genes. Methods for computational prediction of promoters and genes in the entire genome also rely heavily on predetermined data sets used to train their models. This requires collecting a large set of highly accurate promoter sequences.

PromoSer is a web-based service aimed specifically at the extraction of a large number of promoter sequences from mammalian genomes. To identify the transcription start site (TSS) of a gene, we map all available mRNA and EST sequence data onto the genome and track the overlapping alignments (denoted as a cluster) to determine the furthest possible extension to these sequences and hence determine the TSS. In many cases, our data set is enriched with full-length mRNA sequences produced by cap-trapping and oligo capping methods, providing higher confidence in our predictions.

PromoSer is easy to use. Just provide a list of GenBank accession ids to identify the genes of interest and enter the range required flanking the TSS. PromoSer will process the input and return the required regions as a multi-FASTA format text file.

Please use the following citation for PromoSer:

    Anason S. Halees, Dmitriy Leyfer, and Zhiping Weng
    Promoser: A Larger-scale Mammalian Promoter and Transcription Start Site Identification Service.
    Nucl. Acids. Res. 2003 31: 3554-3559. [Abstract] [Full Text]

The current release of PromoSer is 3.0 and is based on the following genomic releases:

    Human (Homo sapiens): July 2003 (hg16) - A finished release.
    Mouse (Mus musculus): Oct 2003 (mm4) - A draft release.
    Rat (Rattus norvegicus): June 2003 (rn3) - A draft release.
PromoSer has analyzed all relevant GenBank accessions up to Feb 4, 2004. For a summary of the contents and overall performance of PromoSer, see this page.

Protein Engineering