Method for rapidly removing vector sequences in batches based on perl language

A sequence and carrier technology, which is applied in the field of fast batch removal of carrier sequences based on perl language, can solve problems such as time-consuming, laborious, error-prone, and slow work efficiency

Pending Publication Date: 2020-10-23
SHANGHAI PASSION BIOTECHNOLOGY CO LTD
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Benefits of technology

This technology allows quick removal from large amounts of sequence data quickly without affecting its accuracy or processing speed any more than it needs them all over again.

Problems solved by technology

This patented technical problem addressed in this patents relates to complicated nucleic acid samples such as those found in medicine researches where accurate data cannot currently be achieved due to difficulties associated with direct sequential testing techniques like Sanger's technique. Current approaches involve manually removing unnecessary vectors before analyzing them, leading to increased errors and low working efficacy rates.

Method used

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  • Method for rapidly removing vector sequences in batches based on perl language
  • Method for rapidly removing vector sequences in batches based on perl language
  • Method for rapidly removing vector sequences in batches based on perl language

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0027] Embodiment 1 specifically comprises the steps:

[0028] Step 1: Use the file in the text format of the sequencing result, or use the Chromas software to convert the sequencing peak map file;

[0029] File→Batch or Processing→Batch or Export→Save or as type→Fasta→Export, and finally get the conversion file of .fa.

[0030] Step 2: Perform specific removal of the vector sequence by locating and matching the sequences at both ends of the vector insertion site;

[0031] Compare and match the sequence at both ends of the vector insertion site set in the script with the sequence in the sequencing result, completely match or match more than 7 bases, the default intermediate sequence is the target sequence, and intercept the sequence.

[0032] Step 3: Filter unqualified sequencing results;

[0033] The sequence at both ends of the vector insertion site set in the script is compared and matched with the sequence in the sequencing result. If there is no complete match or the match

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Abstract

The invention discloses a method for rapidly removing vector sequences in batches based on perl language. The method comprises the following steps: 1, performing format conversion on a sequencing result text format file or a sequencing peak graph file by using Chromas software; step 2, carrying out specific removal on the vector sequences by positioning and matching sequences at two ends of vectorinsertion sites, and comparing and matching sequences at two ends of a vector insertion site set in a script with sequences in a sequencing result; 3, filtering out unqualified sequencing results, wherein sequences at two ends of the vector insertion site set in the script with the sequences in the sequencing result are compared and matched, and sequences which are not in complete matching or having no more than 7 matched basic groups are defaulted as unqualified sequences and are not output; and 4, outputting a vector-free sequence result, and adjusting an output result according to the directivity of the sequences at the two ends of the vector insertion sites. According to the method, multiple sequences can be removed at a time, and the number of data volume processed at a time is not limited.

Description

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Claims

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Application Information

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Owner SHANGHAI PASSION BIOTECHNOLOGY CO LTD
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