Frequently Asked Questions

Questions

FGI BLASTing Miscellaneous

Answers

FGI
  • What is the FGI?
    FGI stands for the Fungal Genome Initiative. Please check the HISTORY page for details
  • What is the goal of the FGI?
    The goal of the Fungal Genome Initiative is to provide the sequence of key organisms and their related species across the fungal kingdom and thereby lay the foundation for work in medicine, agriculture, and industry through comparative studies. Organisms are selected for sequencing as part of a comprehensive plan to understand the biology and evolutionary history of the entire fungal kingdom.
  • What is the organization of the FGI?
    The FGI represents a partnership between Broad Institute of Harvard and MIT and the broad research community, and is directed by a Steering Committee of fungal biologists.
  • What is the FGI Steering Committee?
    The FGI Steering Committee consists of academic and industrial fungal scientists as well as those with experience in genome sequencing and analysis. Please check HISTORY page for details.
  • What is the funding resource for the FGI?
    So far, the FGI fungal sequencing has been supported by NHGRI, NSF and USDA.
  • How are the sequence targets selected?
    The fungal sequencing candidates are nominated by any interested party and are reviewed by the FGI steering committee for selection of the sequence targets. You can submit your nominations on-line using the FGI Candidate Submission Form or send your comment to fgi_comment@broadinstitute.org.
  • What are the principles for the selection of sequence targets?
    The primary selection criteria are:

    a) Importance of the organism in human health and commercial activities.
    b) Value of the organism as a tool for comparative studies of fungal diversity and evolution.
    c) Presence of genetic resources and an established research community.
  • What are the fungal genomes sequenced through the FGI?
    Please check the STATUS page for details
BLASTing
  • 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.
  • 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.
  • What sequences can I BLAST against?
    You can BLAST your query sequence against all the fungal genome assemblies produced at Broad including S. Cerevisiae, and S. pombe, or blast against individual genomes.
  • Why do I get the message "ERROR: BLASTSetUpSearch: Unable to calculate Karlin-Altschul params, check query sequence"?
    From the NCBI Blast FAQ:
    This will happen if your entire query sequence has been masked by low complexity filtering. You will need to turn filtering off to get hits. For further information on filtering, please read the sections of the BLAST FAQs on Q: What is low-complexity sequence? and also Q: After running a search why do I see a string of "X"s (or "N"s) in my query sequence that I did not put there?
  • After running a search why do I see a string of "X"s (or "N"s) in my query sequence that I did not put there?
    From the NCBI Blast FAQ:
    You are seeing the result of automatic filtering of your query for low-complexity sequence that is performed to prevent artifactual hits. The filter substitutes any low-complexity sequence that it finds with the letter "N" in nucleotide sequence (e.g., "NNNNNNNNNNNNN") or the letter "X" in protein sequences (e.g., "XXXXXXXXX"). Low-complexity regions can result in high scores that reflect compositional bias rather than significant position-by-position alignment (Wootton & Federhen, 1996). Filter programs can eliminate these potentially confounding matches from the blast reports, leaving regions whose BLAST statistics reflect the specificity of their parities alignment. Queries searched with the blastn program are filtered with DUST. The other BLAST programs use SEG.
  • What is low-complexity sequence?
    From the NCBI Blast FAQ:
    Regions with low-complexity sequence have an unusual composition and this can create problems in sequence similarity searching (Wootton & Federhen, 1996). Low-complexity sequence can often be recognized by visual inspection. For example, the protein sequence PPCDPPPPPKDKKKKDDGPP has low complexity and so does the nucleotide sequence AAATAAAAAAAATAAAAAAT. Filters are used to remove low-complexity sequence because it can cause artifactual hits (please also see Q: After running a search why do I see a string of "X"s (or "N"s) in my query sequence that I did not put there?)

    In BLAST searches performed without a filter, often certain hits will be reported with high scores only because of the presence of a low-complexity region. Most often, this type of match cannot be thought of as the result of homology shared by the sequences. Rather, it is as if the low-complexity region is "sticky" and is pulling out many sequences that are not truly related.

Miscellaneous
  • What's the Broad Institute?
    Broad Institute of Harvard and MIT, http://www.broadinstitute.org
  • Who do I contact with questions about the sequencing?
    For additional help or to send feedback about the website, please email annotation-webmaster@broadinstitute.org.
  • Where are the beautiful photos from?
    The photos on the front page come courtesy of: (left to right)
    • A. nidulans mutants. Courtesy of Ron Morris, University of Medicine and Dentistry of New Jersey.
    • A. nidulans Conidiophore bearing Conidia. Courtesy of Ron Morris.
    • Coprinus cinereus fruiting in petri dish. Courtesy of Patricia Pukkila, University of North Carolina.
    • Ustilago maydis. Courtesy of the Maize Genetics and Genomics Database, University of Missouri,
      and the International Maize and Wheat Improvement Center (CIMMYT).
    • Zygote with a contributing thalli of Chytrid. Courtesy of Yajuan Liu, University of Washington.