Assignment 1

 

(1) Database : The Eukaryotic Promoter Database (EPD)

http://www.epd.isb-sib.ch/

  1. The Eukaryotic Promoter Database is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references.
    EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis.
  2. An EPD entry contains the following types of information:
Each entry has an ID and an accession number. The description typically includes a gene or a gene product name. The exceptions are promoters used for transcription of several genes, such as the Adenovirus major late promoter.

 

(2)Analysis Tool : BLAST

http://www.ncbi.nlm.nih.gov/BLAST/
  1. BLASTR (Basic Local Alignment Search Tool) is a set of similarity search programs designed to explore all of the available sequence databases regardless of whether the query is protein or DNA. The BLAST programs have been designed for speed, with a minimal sacrifice of sensitivity to distant sequence relationships. The scores assigned in a BLAST search have a well-defined statistical interpretation, making real matches easier to distinguish from random background hits. BLAST uses a heuristic algorithm which seeks local as opposed to global alignments and is therefore able to detect relationships among sequences which share only isolated regions of similarity (Altschul et al., 1990). For a better understanding of BLAST you can refer to the BLAST Course which explains the basics of the BLAST algorithm.
  2. Function:

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