Detail publikace

Overlap detection for a genome assembly based on genomic signal processing

Originální název

Overlap detection for a genome assembly based on genomic signal processing

Anglický název

Overlap detection for a genome assembly based on genomic signal processing

Jazyk

en

Originální abstrakt

Although the genome sequences of most studied organisms, like human, E. coli, and others are already known, de novo genome sequencing remains popular as a majority of genomes remains unknown. Unfortunately, sequencing machines are able to read only short fragments of DNA. Therefore, one of the basic steps in reconstructing novel genomes lies in putting these pieces of DNA, called ‘reads’, together into complete genome sequences using a process known as genome assembly. Reads joining, however, requires efficient detection of their overlaps. This is commonly performed by comparing the particular characters (A, C, G, T) of the reads using string processing techniques. In this paper, we present an alternative way of detecting overlaps using genomic signal processing. Unlike string comparison, numerical phase signals reflect the complementarity of double stranded DNA making the signal ideal for effective strand independent overlap detection using covariance with high accuracy.

Anglický abstrakt

Although the genome sequences of most studied organisms, like human, E. coli, and others are already known, de novo genome sequencing remains popular as a majority of genomes remains unknown. Unfortunately, sequencing machines are able to read only short fragments of DNA. Therefore, one of the basic steps in reconstructing novel genomes lies in putting these pieces of DNA, called ‘reads’, together into complete genome sequences using a process known as genome assembly. Reads joining, however, requires efficient detection of their overlaps. This is commonly performed by comparing the particular characters (A, C, G, T) of the reads using string processing techniques. In this paper, we present an alternative way of detecting overlaps using genomic signal processing. Unlike string comparison, numerical phase signals reflect the complementarity of double stranded DNA making the signal ideal for effective strand independent overlap detection using covariance with high accuracy.

BibTex


@inproceedings{BUT141452,
  author="Robin {Jugas} and Karel {Sedlář} and Helena {Škutková} and Martin {Vítek}",
  title="Overlap detection for a genome assembly based on genomic signal processing",
  annote="Although the genome sequences of most studied
organisms, like human, E. coli, and others are already known,
de novo genome sequencing remains popular as a majority of
genomes remains unknown. Unfortunately, sequencing
machines are able to read only short fragments of DNA.
Therefore, one of the basic steps in reconstructing novel
genomes lies in putting these pieces of DNA, called ‘reads’,
together into complete genome sequences using a process known
as genome assembly. Reads joining, however, requires efficient
detection of their overlaps. This is commonly performed by
comparing the particular characters (A, C, G, T) of the reads
using string processing techniques. In this paper, we present an
alternative way of detecting overlaps using genomic signal
processing. Unlike string comparison, numerical phase signals
reflect the complementarity of double stranded DNA making
the signal ideal for effective strand independent overlap
detection using covariance with high accuracy.",
  address="IEEE Computer Society",
  booktitle="2017 IEEE 30th International Symposium
on Computer-Based Medical Systems",
  chapter="141452",
  doi="10.1109/CBMS.2017.140",
  howpublished="online",
  institution="IEEE Computer Society",
  number="30",
  year="2017",
  month="july",
  pages="301--305",
  publisher="IEEE Computer Society",
  type="conference paper"
}