Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • feature response curve explanation

    Hi,

    Could someone provide a more layman's explanation of how to interpret the feature response curve metric to assess assemblies?
    The following explanation is found at http://bioinformatics.nyu.edu/wordpr...esponse-curve/, and the original paper at http://www.plosone.org/article/info%...l.pone.0019175, but I'm still having trouble understanding. Thank you in advance.

    Inspired by the standard receiver operating characteristic (ROC) curve, the Feature-Response curve characterizes the sensitivity (coverage) of the sequence assembler output (contigs) as a function of its discrimination threshold (number of features/errors). The AMOS package provides an automated assembly validation pipeline called amosvalidate that analyzes the output of an assembler using a variety of assembly quality metrics (or features). Examples of features include: (M) mate-pair orientations and separations, (K) repeat content by k-mer analysis, (C) depth-of-coverage, (P) correlated polymorphism in the read alignments, and (B) read alignment breakpoints to identify structurally suspicious regions of the assembly. After running amosvalidate on the output of the assembler, each contig is assigned a number of features that correspond to doubtful regions of the sequence. Given any such set of features, the response (quality) of the assembler output is then analyzed as a function of the maximum number of possible errors (features) allowed in the contigs. More specifically, for a fixed feature threshold φ, the contigs are sorted by size and, starting from the longest, only those contigs are tallied, if their sum of features is . For this set of contigs, the corresponding approximate genome coverage is computed, leading to a single point of the Feature-Response curve.
    Last edited by Kennels; 06-05-2013, 10:21 PM.

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...
    04-22-2024, 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, Yesterday, 11:49 AM
0 responses
13 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-24-2024, 08:47 AM
0 responses
16 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-11-2024, 12:08 PM
0 responses
61 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 10:19 PM
0 responses
60 views
0 likes
Last Post seqadmin  
Working...
X