Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Filter 18s sequences using HMMs?

    Hi all,

    Apologies if this has been covered before but I'm fairly new to this and can't seem to find an answer to my question anywhere,

    I've been using rRNAselector to filter out 16s fragments from my 250bp PE illumina shotgun reads with good success, however it is limited in that it can only filter out reads using the pre-packaged 16s HMM profiles that come with the program.

    I'm now wondering if anyone knows of a similar tool which can use custom built HMM profiles to filter out reads from metagenomic libraries, as I'd like to try the same thing with 18s and possibly functional gene fragments. Is it as simple as building a profile with hmmbuild and using hmmalign to gt the reads which hit and filtering those out?

    One thing I like about rRNAselector is that it trims all non-16s sequences from the reads which hit too (which makes it useful for downstream analysis in qiime) if anyone knows of a tool which can do this too I'd be eternally grateful!

    any help at all would be great,

    Many thanks,

    Jonny

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
8 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 06:07 PM
0 responses
8 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