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Method for Structural Annotation and Alignment Assessment of Full-Length Transcripts

A technology for comparing results and transcripts, applied in genomics, instrumentation, proteomics, etc. It can solve the problems of redundant and unclear matchAnnot results, and achieve the effect of optimizing the display method.

Active Publication Date: 2020-10-23
南京派森诺基因科技有限公司
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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

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  • Method for Structural Annotation and Alignment Assessment of Full-Length Transcripts

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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...

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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

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G16B20/00
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
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