Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Burrows Wheeler Transform

    I wrote an introductory post on Burrows Wheeler Transform that powers many efficient search programs such as Bowtie, BWA and SOAP2.



    We usually do not cover topics that are explained everywhere else, and BWT is over 20 years old - so old that it even has a wiki page. However, I could not find a simple explanation of LF mapping property anywhere. LF mapping is used by search programs to map short reads onto reference sequence.

    Is it important to learn how the algorithm works to use Bowtie and BWA? I do not think so, but I enjoy shows like car-talk without ever intending to get under the car
    Last edited by samanta; 10-04-2011, 11:06 AM.
    http://homolog.us

  • #2
    Posted part II -



    I worked out another example, and also explained how the search is really done.
    http://homolog.us

    Comment


    • #3
      Great stuff, is part III going to show the auxiliary data structures for an FM-index (occurrence array etc.)?

      Comment


      • #4
        Originally posted by nilshomer View Post
        Great stuff, is part III going to show the auxiliary data structures for an FM-index (occurrence array etc.)?

        Thank you !! Still undecided about where to go next. Everyone wants to know how electricity works, but not operations of three phase, or Y-delta, or AC motor.
        http://homolog.us

        Comment


        • #5
          Originally posted by samanta View Post
          Thank you !! Still undecided about where to go next. Everyone wants to know how electricity works, but not operations of three phase, or Y-delta, or AC motor.
          Ask my dog, named Tesla. Anyhow, I would be happy to contribute as I think it would go a long way to those interested.

          Comment

          Latest Articles

          Collapse

          • seqadmin
            Essential Discoveries and Tools in Epitranscriptomics
            by seqadmin


            The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist on Modified Bases...
            Yesterday, 07:01 AM
          • seqadmin
            Current Approaches to Protein Sequencing
            by seqadmin


            Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
            04-04-2024, 04:25 PM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, 04-11-2024, 12:08 PM
          0 responses
          39 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 04-10-2024, 10:19 PM
          0 responses
          41 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 04-10-2024, 09:21 AM
          0 responses
          35 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 04-04-2024, 09:00 AM
          0 responses
          55 views
          0 likes
          Last Post seqadmin  
          Working...
          X