two efficient techniques to find approximate overlaps between sequences
Clicks: 109
ID: 237014
2017
Article Quality & Performance Metrics
Overall Quality
Not rated
Combines reader engagement with the AI quality analysis. This
article has not been analysed, so there is no overall score —
reader engagement is measured and shown alongside.
Reader Engagement
Emerging Content
30.0
/100
109 views
22 readers
AI Quality Assessment
Not analyzed
Readership in this journal
EmergingRanked #1,097 of 1,324 articles by views in spectrochimica acta - part a: molecular and biomolecular spectroscopy
Most read
Least read
Bar heights use a square-root scale. Only the 120 most-read articles are drawn; the journal has 1,324 in total.
Mint this article as an NFT
Not yet mintedCreate a permanent, verifiable on-chain record of this article on the Scimatic Network. The NFT is held in your Journament account, and you can withdraw it to your own wallet at any time.
5
SUSD
one-off · no wallet required
Abstract
The next-generation sequencing (NGS) technology outputs a huge number of sequences (reads) that require further processing. After applying prefiltering techniques in order to eliminate redundancy and to correct erroneous reads, an overlap-based assembler typically finds the longest exact suffix-prefix match between each ordered pair of the input reads. However, another trend has been evolving for the purpose of solving an approximate version of the overlap problem. The main benefit of this direction is the ability to skip time-consuming error-detecting techniques which are applied in the prefiltering stage. In this work, we present and compare two techniques to solve the approximate overlap problem. The first adapts a compact prefix tree to efficiently solve the approximate all-pairs suffix-prefix problem, while the other utilizes a well-known principle, namely, the pigeonhole principle, to identify a potential overlap match in order to ultimately solve the same problem. Our results show that our solution using the pigeonhole principle has better space and time consumption over an FM-based solution, while our solution based on prefix tree has the best space consumption between all three solutions. The number of mismatches (hamming distance) is used to define the approximate matching between strings in our work.
| Reference Key |
rachid2017biomedtwo
Use this key to autocite in the manuscript while using
SciMatic Manuscript Manager or Thesis Manager
|
|---|---|
| Authors | ;Maan Haj Rachid |
| Journal | spectrochimica acta - part a: molecular and biomolecular spectroscopy |
| Year | 2017 |
| DOI |
10.1155/2017/2731385
|
| URL | |
| Keywords |
Citations
No citations found. To add a citation, contact the admin at info@scimatic.org
Comments
No comments yet. Be the first to comment on this article.