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Asked by Avani B to Kim on 3 Jun 2020.
Question: Do you use any of GENBANK, FASTA FILE or EMBL formats when manipulating DNA sequences?
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Kim Liu answered on 3 Jun 2020:
Wow this is a v. specialised question 🙂 Most of all I use a file format known as FASTQ for manipulating my own sequencing data; these are the raw data directly from the sequencer and contain sequencing quality scores. I prefer to download FASTA if I want to align to a reference genome, but actually I don’t do this so often in my work because I don’t often sequence large portions of a genome at once. I have never tried using GENBANK and EMBL – these are specialised file formats created by certain institutions (US National Institute of Health and European Bioinformatics Institutes). How did you come across these file formats? Are you doing a sequencing project?
Comments
Avani B commented on :
Oh right! Actually, I did an online accredited course on Bioinformatics by the Wellcome Genome Campus and enjoyed it very much! No, unfortunately I’m not doing a sequencing project. Do you you know of any more websites that are good for sequencing or even FASTA ( I’d like to try or have a look ) or apps even?
Kim commented on :
That’s awesome! If you are interested in any biological research, being able to do your own bioinformatics is unbelievably useful 🙂 So I use a thing called Snapgene to view DNA files, because as I said, I generally look at small bits of DNA (single genes and so on). It’s a very useful tool for helping you design molecular biology experiments – https://www.snapgene.com/ To look at the whole genome, I know my colleagues use a thing called IGV (https://igv.org/app/), which should be free to use as a web app and download. It allows you to view genomes and their annotations (e.g. gene labels).
Sequencing data does look quite weird when you first look through, partially because you have to zoom in a lot to get to seeing letters, and also because sequencing experiments often like to represent sequencing reads as peaks (maybe you saw that in your course?). Let’s keep talking, if I am not so clear, or if you want to know more! (Or, of course, ask the rest of the community 🙂 )
Gabriela commented on :
I do. In fact I am currently learning programming in order to use these kinds of data, during lockdown, to formulate hypothesis and design experiments. In the main most platforms these days have user-friendly interfaces which allows the user to harvest the information that they need from such databases without programming skills, but it is much better to be able to do it yourself so that you have control over the analysis. I would definitely recommend any budding biomedical scientists to engage with programming to further their careers.
Ailith commented on :
Hi Avani, I’m a bioinformatician. Happy to answer any specific questions you have! Have you heard of Galaxy? https://usegalaxy.eu/ Check it out! You can use it to process sequencing data from raw fasta files all the way through to interpreting genetic variants to understand their potential roles in disease. IGV as Kim said is a really cool tool to explore bam files (so sequencing reads aligned to the reference genome). You can also look at files containing genetic variants (vcf format) in IGV.
Luke commented on :
Hi Avani, there is also a new tool called https://benchling.com/signin/welcome which is really intuitive for looking at small bits of DNA, primer design and for looking at plasmids. Its free and has a nice tutorial if you’re interested in looking around some more