Alignment method, apparatus and system

An alignment and ratio technology, applied in the field of sequence alignment device and sequence alignment system, can solve the problem that the alignment method needs to be improved, and achieve the effect of high sensitivity and accuracy, efficient and precise positioning

Active Publication Date: 2017-11-28
GENEMIND BIOSCIENCES CO LTD
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  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

[0004] Sensitivity, comparison time and / or comparison efficiency for specific types of data, existing comparison methods need to be improved

Method used

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  • Alignment method, apparatus and system
  • Alignment method, apparatus and system
  • Alignment method, apparatus and system

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Embodiment Construction

[0021] Embodiments of the present invention are described in detail below, examples of which are shown in the drawings, wherein the same or similar reference numerals designate the same or similar elements or elements having the same or similar functions throughout. The embodiments described below by referring to the figures are exemplary only for explaining the present invention and should not be construed as limiting the present invention.

[0022] In the description of the present invention, the so-called "first" and "second" are used for description purposes only, and cannot be understood as indicating or implying relative importance and / or sequence.

[0023] The so-called "connection" and "connection" should be understood in a broad sense, for example, it can be a fixed connection, a detachable connection, or an integral connection; it can be a mechanical connection or an electrical connection; it can be a direct connection, It can also be indirectly connected through an ...

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Abstract

The invention discloses an alignment method, apparatus and system. The alignment method comprises converting each read into a set of short fragments corresponding to the read, and obtaining multiple sets of short fragments; determining corresponding positions of the short fragments in a reference library so as to obtain a first positioning result, wherein the reference library is a Hash table constructed on basis of a reference sequence, the reference library includes a plurality of entries, each entry of the reference library is corresponding to a seed sequence, each seed sequence can be matched with at least one sequence fragment on the reference sequence, and a distance between two seed sequences corresponding to two adjacent entries of the reference library on the reference sequence is less than the length of the short fragments; removing the short fragment positioned to any one of the adjacent entries of the reference library in the first positioning result, and obtaining a second positioning result; and performing extending based on common parts of the short fragments from the same read in the second positioning result so as to obtaining an alignment result of the read. Sequencing data can be processed and positioned efficiently and accurately by the alignment method.

Description

technical field [0001] The invention relates to the field of data processing, in particular to a sequence comparison method, a sequence comparison device and a sequence comparison system. Background technique [0002] In biological data processing and analysis, comparison, as the basic link of biological information analysis, puts forward certain requirements for time and efficiency, and different comparison models and algorithms have different sensitivities and accuracy. [0003] Currently mainstream alignment software such as bwa, bowtie, and soap are mainly developed for sequences generated by next-generation sequencing platforms, while software such as blast and mapq are mainly developed for long sequences. [0004] Sensitivity, comparison time and / or comparison efficiency for specific types of data, existing comparison methods need to be improved. Contents of the invention [0005] The embodiments of the present invention aim at at least solving one of the technical ...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/20G06F19/24
CPCG16B25/00G16B40/00
Inventor 徐伟彬金欢颜钦姜泽飞周志良
Owner GENEMIND BIOSCIENCES CO LTD
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