How to use SNP to construct fingerprint

This article introduces you how to use SNP to build fingerprints, the content is very detailed, interested friends can refer to, hope to be helpful to you.

Use SNP to build fingerprints!

High-throughput sequencing will get a lot of SNP, how to use these SNP is a very important work. Especially when collecting and screening some germplasm resources, we often want to use the least amount of SNP to distinguish as many samples as possible, that is, fingerprint DNA fingerprinting, which is very useful and practical in actual scientific research and production. Today, I would like to share a software-SNPT, which can help you select the SNP combination you want most from thousands of SNPs for fingerprint construction.

Software introduction

SNPT download address: http://www.shigatox.net/stec/cgi-bin/snpt this software can do the analysis:

Indentify unique SNPs profiles and assign sequence types (MST)

Calculate allele frequencies

Find informative SNPs

Calculate D (Index of the Discrininatory Ability)

Find the set (s) of minimum SNPs

Output MST data file in mega and interleaved mega format.

The input file format is as follows: the columns are separated by tab, and the location information of the first behavior SNP on the genome; starting from the second line, the first column is listed as the sample name, followed by the corresponding SNP.

Strain 325 968 2351 4768 4980 6971 9323 1319ARK0000038 G C C G G A G TARK0000056 G C C G G A G TARK0000062 G C C G G A G TARK0000066 G C C G G A G TARK0000069 G C T G G A G T...

Software use

Download the software, the software does not need to install, decompress can be used.

Load the input file.

Calculates the minimum SNP collection.

After the calculation is completed, the text box on the right will be displayed, and the output file will also be displayed here.

Output file:

Each behavior has a sample, each is listed as a marker, and different colors represent different typing.

On how to use SNP to build fingerprints to share here, I hope the above content can be of some help to you, can learn more knowledge. If you think the article is good, you can share it for more people to see.