Take the 2-minute tour ×
Biology Stack Exchange is a question and answer site for biology researchers, academics, and students. It's 100% free, no registration required.

What is the type of data you get when analyzing dna of a person? If you want to store them in a database, what type of field you will need (text,number,hex)? And what should be it's length?

share|improve this question
add comment

3 Answers 3

up vote 3 down vote accepted

Assuming that you are looking at data used to describe the differences for a new individual, as opposed to a human reference genome build:

A fastq file is the typical format of data from a sequencer.

It would require a text field of some sort as they can be quite large, even for single reads. If you had a specific sequencer in mind with very short read you might use a fixed length field for the data column, but its probably not worth it.

After the data is processed, then the data is currently usually exchanged in the form of Variant Call Format files (a vcf file) which only documents differences versus a reference genome build. This fits nicely into an SQL table with relatively small columns.

share|improve this answer
add comment

It will be a simple string of text. The length, however, is completely arbitrary and will depend on the source of your sequence data. Anything from 1 to several billion can be a valid sequence length.

We could help more if you explained where the data is coming from.

share|improve this answer
add comment

Realistically, you aren't going to store the genome as one long string of text. Depending on how you do the sequencing, you probably won't be able to resolve repetitive regions anyway.

What is much more realistic is you will store all the differences you are confident of between the sample and a reference sequence.

If you use some kind of genotyping chip, you'd store the genotypes at each locus.

share|improve this answer
add comment

Your Answer

 
discard

By posting your answer, you agree to the privacy policy and terms of service.

Not the answer you're looking for? Browse other questions tagged or ask your own question.