Unconfigured Ad

Collapse
X
Collapse
 
  • Page of 1
  • Filter
  • Time
  • Show
Clear All
new posts
Previous template Next
  • Kennels
    Senior Member
    • Feb 2011
    • 149
    #1

    question about delta blast warning

    Hi,

    I'm running deltablast with the rpsdb database as CDD v3.1 downloaded off ncbi (I ran makeprofiledb on the raw .pssm's to make applicable for deltablast). I am running into warnings like this:

    ##
    Warning: lcl|Query_9517: Warning: Frequency ratios for PSSM are all zeros, frequency ratios for BLOSUM62 will be used during traceback in composition based statistics
    ##

    It is not for all queries.

    This is the first time I'm running delta blast, so I'm wondering if this is something to worry about when interpreting the output. Does this just mean there wasn't any conserved domains detected for the particular query?

    Any comments greatly appreciated. Thanks.
    Last edited by Kennels; 04-28-2013, 11:14 PM.
    Tags: None
  • klager
    Junior Member
    • Oct 2012
    • 2
    #2
    Yes, the warning comes just because no CDD domain was found. And it's possible to download a cdd_delta.tar.gz from NCBI Blast ftp site, so you don't have to index CDD your self.

    Comment

    • rhinoceros
      Senior Member
      • Apr 2013
      • 372
      #3
      Did you build your db as suggested in this document?
      savetherhino.org

      Comment

      • klager
        Junior Member
        • Oct 2012
        • 2
        #4
        As described in the BLAST 2.26+ Release, there's a special version of the CDD database (cdd_delta) available from the BLAST db directory on the FTP site:

        NCBI News, April 2012 - NCBI News - NCBI Bookshelf
        http://www.ncbi.nlm.nih.gov/books/NBK92578/
        NCBI will present a two-day workshop May 15 and 16, 2012, on the NIH campus in Bethesda, Maryland. The course is free and is open to anyone interested in NCBI resources. The four workshops are Sequences, Genomes, and Maps; Proteins, Domains and Structures; NCBI BLAST Services; and Human Variation and Disease Genes. These workshops provide hands-on experience exploring practical examples using tools and databases on the NCBI website. The Discovery Workshops page has more details and a link to register for the course.

        ftp://ftp.ncbi.nih.gov/blast/db/

        No need to build a CDD db

        Comment

        Previous template Next

        Latest Articles

        Collapse
        • SEQadmin2
          Proteomic Platforms: How to Choose the Right Analytical Strategy to Improve Detection and Clinical Applications
          by SEQadmin2


          Proteomics platforms are evolving rapidly, with advances in mass spectrometry and affinity-based approaches expanding what researchers can detect and at what scale. As the field moves toward deeper proteome coverage and clinical applications, scientists face an increasingly complex landscape of tools. This article will explore how researchers are navigating these choices to find the right platform for their work.

          The systematic characterization of the human proteome has          ...
          07-20-2026, 11:48 AM
        • SEQadmin2
          Advanced Sequencing Platforms Tackle Neuroscience’s Toughest Genomics Problems
          by SEQadmin2



          Genomics studies in neuroscience face a special challenge due to the brain’s complexity and scarcity of samples. Mapping changes in cell type and state using conventional next-generation sequencing methods remains challenging. Advances in technologies like single-cell sequencing, spatial transcriptomics, and long-read sequencing have opened the door to deeper studies of the brain and diseases like Alzheimer’s, amyotrophic lateral sclerosis (ALS), and schizophrenia.
          ...
          07-09-2026, 11:10 AM
        • SEQadmin2
          Cancer Drug Resistance: The Lingering Barrier to Rising Survival
          by SEQadmin2



          Cancer survival rates have significantly increased in the last few decades in the United States, reaching a combined 70% 5-year survival rate by 2021. Behind this number, there are years of research to find new therapies, drug targets, and early detection methods. But there is one core challenge that keeps slowing down these advances, and it’s about drug resistance.

          There is no single reason why many patients don’t respond to treatment as expected. Cancer is...
          07-08-2026, 05:17 AM
        View All

        ad_right_rmr

        Collapse

        News

        Collapse
        Topics Statistics Last Post
        Study Captures the First Moments of DNA Replication by SEQadmin2
        Started by SEQadmin2, 07-24-2026, 12:17 PM
        0 responses
        19 views
        0 reactions
        		 Last Post SEQadmin2
        by SEQadmin2
        07-24-2026, 12:17 PM  
        Chemotherapy Leaves Detectable DNA Signatures in Childhood Tumors by SEQadmin2
        Started by SEQadmin2, 07-23-2026, 11:41 AM
        0 responses
        19 views
        0 reactions
        		 Last Post SEQadmin2
        by SEQadmin2
        07-23-2026, 11:41 AM  
        Single-Cell Atlases Skew Toward European Ancestry, Analysis Finds by SEQadmin2
        Started by SEQadmin2, 07-20-2026, 11:10 AM
        0 responses
        25 views
        0 reactions
        		 Last Post SEQadmin2
        by SEQadmin2
        07-20-2026, 11:10 AM  
        UC San Diego Bioengineers Map Gene Function in Human Stem Cells by SEQadmin2
        Started by SEQadmin2, 07-13-2026, 10:26 AM
        0 responses
        38 views
        0 reactions
        		 Last Post SEQadmin2
        by SEQadmin2
        07-13-2026, 10:26 AM  
        View All
        Working...