Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Haplotypes reconstruction using 454 data (single-end reads)

    Hi everyone,

    I have samples of viral genomes (wild samples). Each sample are possibly composed by dozens of structurally different genomes (in terms of indels, SNPs, inversions, transpositions, etc), and I have a reference genome of this virus.

    I have 454 data from these samples, in which the reads have an average of 400 bp. I think that it'll be very hard (perhaps impossible) to determine which haplotype belongs to which individual genome in each sample (supported by the correct overlapping at the ends of the reads in a contig, in an stringent assembly)... Also, these viruses have several in tandem repeated regions, which beconme this assembly more complicated.

    Is there any bioinformatics approach to reconstruct the most frequent structural variants from each sample, and also determine the presence or absent of specific haplotypes, without perform extra molecular cloning experiments?

    Best!
    Last edited by AFBrito; 08-13-2012, 07:32 AM.

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