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 big is the Methanosarcina genome?
      5,751,492 base pairs

    3. What strain was sequenced?
      The Methanosarcina acetivorans strain C2A was grown in single cell morphology47 at 35°C in HS broth medium containing 125 mM methanol plus 40 mM sodium acetate (HS-MA medium)48.

    4. What is the current state of the sequenced genome?
      We present the finished genome sequence.

  • Annotation
    1. Is gene XXX annotated in the sequence?
      You can find genes based on name, locus, symbol abbreviation, genbank number, protein family domain, and cellular functional category.

  • Downloading
    1. What format is the download file in?
      The genome data is pure text in multiple FASTA format. The text file has been compressed using gzip. To uncompress the file: 

      2.      gunzip methanosarcina.fasta.gz
    2. 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.

    3. The download fails. What should I do?
      Downloading through the browser uses the http protocol. You can also try accessing the ftp site directly via the URL:

  • BLASTing
    1. Why is my BLAST job taking so long?
      BLAST jobs are queued and handled with other internal Broad processes in a general Load Sharing Facility. The delay for receiving your BLAST results depends on the current load.

    2. Why are my BLAST results split into multiple email messages?
      Some email programs are configured with a maximum message size and will automatically split large files into smaller pieces. If this is undesirable, you will need to reconfigure your email program.
  • Genome Browser

    1. Does the Genome Browser Java applet run on Macintosh computers?
      We are pleased to announce that the Genome Browser can now run on both Windows and Macintosh platforms.

      Requirements for Windows:
      Windows 9x & NT platforms or better
      Java 1.4
      Netscape Navigator 4+, Internet Explorer 5+, Mozilla 1.* or other browser that can display Java applets

      Requirements for Macintosh:
      OS X
      Java 1.4 (Software Update)
      Safari

  • 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:
        Methanosarcina 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, please contact annotation-info@broad.mit.edu.
      Send feedback about the website to annotation-webmaster@broad.mit.edu.

    4. Where are the beautiful photos from?
      The black & photo photos of Methanosarcina acetivorans are from Professor Herbert Fang, The University of Hong Kong, http://www.croucher.org.hk/research.asp. Other photos are from the Broad.