Structure annotation and comparison result evaluation method of full-length transcript

A technology for comparing results and transcripts, applied in special data processing applications, instruments, electrical digital data processing, etc., it can solve the problems of redundant and unclear matchAnnot results, and achieve the effect of optimizing the display method.

Active Publication Date: 2018-01-09
南京派森诺基因科技有限公司
View PDF5 Cites 0 Cited by
  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

The evaluation method of the comparison results has the following problems: 1) matchAnnot has requirements for input files, and errors may be reported when using conventional gtf and sam files; 2) the results of matchAnnot are redundant and not clear enough

Method used

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
View more

Image

Smart Image Click on the blue labels to locate them in the text.
Viewing Examples
Smart Image
  • Structure annotation and comparison result evaluation method of full-length transcript

Examples

Experimental program
Comparison scheme
Effect test

Embodiment Construction

[0012] see figure 1 , the comparison result evaluation and gene structure annotation method, including the following steps:

[0013] (1) Obtain the chromosome ID shared by the reference genome annotation gtf file and the full-length transcriptome and reference genome comparison result sam file;

[0014] (2) Screen the entries of non-common chromosomes compared in the sam file, sort them out and output them to no_annotation.txt (this part of the full-length transcript can be supplemented with annotations without reference genome annotation to obtain new genes), and compared The entries of the shared chromosomes are output to tmp.sam;

[0015] (3) Use matchAnnot software for structural annotation and comparison result evaluation, tmp.sam file and gtf file as input files;

[0016] (4) Organize the matchAnnot results, output the polyA motif of the full-length transcript separately to polyA_motif.txt, extract the best matching reference gene and reference transcript information f...

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to view more

PUM

No PUM Login to view more

Abstract

The invention discloses a structure annotation and comparison result evaluation method of a full-length transcript. According to the disclosed comparison result evaluation and gene structure annotation method, matchAnnot software is used, an effect of a script is to modify an existing annotation gtf file and a sam file according to a format required by the matchAnnot software, the matchAnnot is used for structure annotation and comparison result evaluation, a presentation mode of a matchAnnot result is optimized, and counting is carried out.

Description

technical field [0001] The invention relates to the field of biotechnology, in particular to a method for evaluating the structure annotation and comparison results of full-length transcripts. Background technique [0002] Structural annotation refers to the prediction of the primary structure of the full-length transcript based on the comparison results of the full-length transcript and the reference genome, and the evaluation of the comparison result refers to the comparison of the predicted full-length transcript structure with the known gene structure The results, used to evaluate the alignment of full-length transcripts to the reference genome. The current evaluation method for structural annotation and alignment results of full-length transcripts is directly evaluated by matchAnnot. The evaluation method of the comparison results has the following problems: 1) matchAnnot has requirements for input files, and errors may be reported when using conventional gtf and sam f...

Claims

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to view more

Application Information

Patent Timeline
no application Login to view more
Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/18
Inventor 王智健简洁姜丽荣孙子奎
Owner 南京派森诺基因科技有限公司
Who we serve
  • R&D Engineer
  • R&D Manager
  • IP Professional
Why Eureka
  • Industry Leading Data Capabilities
  • Powerful AI technology
  • Patent DNA Extraction
Social media
Try Eureka
PatSnap group products

Browse by: Latest US Patents, China's latest patents, Technical Efficacy Thesaurus, Application Domain, Technology Topic.

© 2024 PatSnap. All rights reserved.Legal|Privacy policy|Modern Slavery Act Transparency Statement|Sitemap