Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • colindaven
    replied
    GMAP might be suitable for your purposes (transcript mapping to GFF3), and is a lot quicker with good parallelization.

    Leave a comment:


  • sandesh
    replied
    Originally posted by Blahah404 View Post
    exonerate is simply a slow program. You can split the query file up into 32 files and run 32 exonerate commands simultaneously, then concatenate the results.

    exonerate comes with a a tool, fastasplit, for this purpose

    Thanks
    I tried that too. I made 100 parts. Running single file took more then 3 days and stopped, which means more then 300 days to go.

    Leave a comment:


  • Blahah404
    replied
    exonerate is simply a slow program. You can split the query file up into 32 files and run 32 exonerate commands simultaneously, then concatenate the results.

    exonerate comes with a a tool, fastasplit, for this purpose

    Leave a comment:


  • sandesh
    replied
    I tried exonerate-server too. This one is also slow.

    Leave a comment:


  • atcghelix
    replied
    I would try running it in server-client mode:

    Leave a comment:


  • sandesh
    started a topic exonerate - how to use multiple cores?

    exonerate - how to use multiple cores?

    Hello,
    I used this command to run exonerate:

    exonerate -m p2g -q uniref90_modified.fasta -t all_LGs/PcapLG_18.fasta --softmasktarget yes --showvulgar no --showalignment no --showtargetgff yes --showquerygff no --percent 80 " > LG18_exonerate_pcap.gff

    This only use one core. I have 32 cores.
    It's getting too slow.

    Thanks

Latest Articles

Collapse

  • seqadmin
    The Impact of AI in Genomic Medicine
    by seqadmin



    Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
    02-26-2024, 02:07 PM
  • 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

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 02-28-2024, 06:12 AM
0 responses
27 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-23-2024, 04:11 PM
0 responses
74 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-21-2024, 08:52 AM
0 responses
81 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-20-2024, 08:57 AM
0 responses
69 views
0 likes
Last Post seqadmin  
Working...
X