Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Adding BLAST+ to Python PATH

    Very new to bioinformatics and I am trying to write a code that will allow me to use a reference geneset (e.g. MLST) and BLAST it against genomes available on Genbank so that I can create datasets of these genesets.

    For example, if I wish to do a multi locus gene comparison for a given genus, I'd like to be able to input my reference gene set, BLAST it against the available genomes and pull the gene sequences (fasta) that match with X% ID from the genome.

    The reason I thought to do a BLAST-extraction is because some of the genomes I'm looking through are not annotated.

    My idea is to use the BLAST+ tools to do this, but I cannot call the module in python. I've downloaded the software, but can only call it in terminal (I am using a mac). I am using python 2.7.5 and have added numpy and biopython.

    Could anyone provide some advice for a novice?

    Thanks in advance!

  • #2
    There are a number of options open to you. One of which is to use code that others have written and tested (always a decent first option!). BIGSdb may be useful for you (http://pubmlst.org/software/database/bigsdb/). If you have access to a local Galaxy instance, there may be an MLST workflow available to you. If you're using pubMLST-compatible definitions, then this Python script https://github.com/widdowquinn/scrip...cs/run_MLST.py might do what you want, or serve as an example you can build from.

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Strategies for Sequencing Challenging Samples
      by seqadmin


      Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
      03-22-2024, 06:39 AM
    • seqadmin
      Techniques and Challenges in Conservation Genomics
      by seqadmin



      The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

      Avian Conservation
      Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
      03-08-2024, 10:41 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, Yesterday, 06:37 PM
    0 responses
    7 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, Yesterday, 06:07 PM
    0 responses
    7 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2024, 10:03 AM
    0 responses
    49 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-21-2024, 07:32 AM
    0 responses
    66 views
    0 likes
    Last Post seqadmin  
    Working...
    X