Tetraodon FAQ

Questions

Answers

  • Sequencing
    1. What is whole-genome shotgun sequencing?
      Whole genome shotgun sequencing is a technique for determining the DNA sequence of a genome by randomly shearing the DNA, sequencing multiple overlapping fragments, and inferring the original sequence from fragments that overlap. This method is often used for bacterial genomes or subclones, like cosmids. Additional information from paired end reads, cosmid ends, and other linkage information will be added in future releases. See Assembly for details.
    2. How much has been sequenced?
      Data Version 10/31/01: 2,049,033 reads (estimated 2.5X genome coverage)

    3. What is the current state of the sequenced genome?
      We have sequenced reads but have not yet assembled them into a genome.
    4. Is the Tetraodon genome fully annotated?
      No. We have finished the first phase of shotgun sequencing which produces millions of short fragments termed "sequence reads". These short (~500bp) reads have been submitted to the NCBI trace repository and are available for BLAST search (see below).

      There are future plans to assemble the Tetraodon shotgun sequence into a whole genome assembly. This is a requirement before annotation can even be attempted.

      Plans for annotation of the Tetraodon genome are under discussion and there is currently no time table or funding for such an effort.

  • Searching/BLASTing
    1. How can I search this sequence information?
      We have collaborated with in the Tetraodon sequencing effort with Genoscope, which offers a Blast tool against the read data: http://www.genoscope.cns.fr/proxy/cgi-bin/recherche_kicy.cgi

      The sequenced Tetraodon reads have also been submitted the NCBI trace repository, and you can perform a Trace repository BLAST search at NCBI.

  • Downloading
    1. Why does gunzip tell me the file is not in gzip format?
      Some browsers (like newer versions on Netscape) automatically unzip files after download. If this is the case, you can just rename the file to remove the .gz suffix.
  • Misc
    1. What's the Broad Institute?
      The Eli and Edythe L. Broad Institute is a partnership among MIT, Harvard and affiliated hospitals and the Whitehead Institute for Biomedical Research. Its mission is to create the tools for genomic medicine and make them freely available to the world and to pioneer their application to the study and treatment of disease.

    2. How do I cite the sequence for publication?
      Publications should include the following citation:
        Tetraodon Sequencing Project. Broad Institute of MIT and Harvard (www.broad.mit.edu)

    3. Who do I contact with questions about the sequencing?
      For additional help or to send feedback about the website, please emailannotation-webmaster@broad.mit.edu.
    4. Where are the beautiful photos from?
      See photo credit for details.