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Faq

Questions

• Sequencing
1. What are the basic statistics about the Listeria monocytogenes genomes?
2. How has the sequence been generated for the Listeria monocytogenes project?
3. Will the genomes be finished?
4. How will we know the assembly is correct?
5. What data are available?
6. This sequence release looks different from previous releases, like Neurospora crassa. What's different?
• Misc.
1. How do I cite the sequence for publication?
2. Who do I contact with questions about the sequencing?
3. Who provided the beautiful images that grace the homepage?

Answers

• Sequencing
1. What are the basic statistics about the Listeria monocytogenes genomes?
   

   Information about the size of the individual sequenced genomes, the assembly coverage, and the number of contigs can be found in the Assembly Details section of the What's New page.

2. How has the sequence been generated for the Listeria monocytogenes project?
   

   We have sequenced Listeria genomes using 454 pyrosequencing chemistry by the Whole Genome Shotgun method. Assembly of 454 data is performed with the 454 assembly software. We have chosen to use the 454 process because it avoids the cloning bias that limits coverage of Listeria genomes sequenced by traditional methods, thus yielding better quality assemblies. The current 454 assembly is estimated to cover approximately 95% of the Listeria genome. In contrast, draft shotgun assemblies of Listeria genomes generated by sequencing of bacterially cloned fragments typically cover only 80% of the genome.

3. Will the genomes be finished?
   

   Yes.

4. How will we know the assembly is correct?
   

   Our assembly of the L. monocytogenes genomes will be verified through comparison with available reference genomic sequences.

5. What data are available?
   

   In this version of our data release, all sequence contigs are available. Sequence data can be accessed in several ways: either through a searching with BLASTN or TBLASTN, retrieving of a specific region of the assembly, or by downloading the entire genome. Contig sequences are subject to change throughout this project, so each data release version number will be appended to the contig number as a prefix (e.g. 1.1 denotes assembly version 1, contig #1).

6. This sequence release looks different from previous releases, like Neurospora crassa. What's different?
   

   Important information about this release can be found here.

• Misc.
1. How do I cite the sequence for publication?
   

   Publications should include the following citation: Listeria monocytogenes Sequencing Project. Broad Institute of Harvard and MIT (http://www.broad.mit.edu)

2. Who do I contact with questions about the sequencing?
   

   Please contact us by using the comments form.

3. Who provided the beautiful images that grace the homepage?
   

   The top fluorescence micrograph, provided by Dr. Peter Lauer of Cerus Corp. shows Listeria monocytogenes strain 10403S at 5 hr. post infection in J774 cells. Bacteria (green) were stained with polyclonal anti-listeria O antigen antibody and a FITC secondary. Actin (red) was stained with Rhodamine phalloidin and DNA (blue) was visualized with DAPI.

   The lifecycle diagram and bottom fluorescence micrograph were provided by Professor Daniel Portnoy in the Department of Molecular and Cell Biology at UC Berkeley. A detailed description of the Listeria monocytogenes lifecycle can be found at http://www.textbookofbacteriology.net/Listeria.htmll. The photomicrograph shows a kidney epithelial cell from Potoroo tridactylis infected with Listeria monocytogenes. Filamentous actin is stained red with rhodamine phalloidin. The bacteria are stained green by indirect immunofluorescence with polyclonal antibody raised against Listeria monocytogenes.