Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Prokka Annotation - How to use blast nr DB

    Hi,

    I want to annotate an assembled Pseudomonas Genome (fasta) with prokka.
    I was successfull so far but I'm not sure where the information comes from.

    I first downloaded a related protein-fasta from NCBI and told prokka to use that file with the --protein option.

    Now what is prokka doing when it finds an unknown cds? Where does it search?

    Is it possible to tell prokka to search in a local downloaded nr blast database?
    maybe it is possible to replace or expand the prokka-used databases by the nr blast db? (I recognized the internal prokka dbs and the nr blast db have different file extensions)

    My idea is:
    Search for all cds in my downloaded, related protein-fasta and at the end to search for all unknown cds in the nr blast database.
    Is that possible?
    Last edited by iltisanni; 05-16-2018, 04:53 AM.

Latest Articles

Collapse

  • seqadmin
    Multiomics Techniques Advancing Disease Research
    by seqadmin


    New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

    A major leap in the field has
    ...
    02-08-2024, 06:33 AM
  • seqadmin
    The 3D Genome: New Technologies and Emerging Insights
    by seqadmin


    The study of three-dimensional (3D) genomics explores the spatial structure of genomes and their role in processes like gene expression and DNA replication. By employing innovative technologies, researchers can study these arrangements to discover their role in various biological processes. Scientists continue to find new ways in which the organization of DNA is involved in processes like development1 and disease2.

    Basic Organization and Structure
    Understanding...
    01-22-2024, 03:25 PM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 08:57 AM
0 responses
12 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-14-2024, 09:19 AM
0 responses
43 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-12-2024, 03:37 PM
0 responses
410 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-09-2024, 03:36 PM
0 responses
649 views
0 likes
Last Post seqadmin  
Working...
X