What’s the Answer: (using blat)

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of thecommunity and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

This question seems kind of basic at first, but it covers something we are asked all the time. Why would I use _____ tool or database? There are a lot of tools and databases out there. Sometimes they seem to do the same thing. But in reality, most of bioinformatics tools and databases are more like overlapping Venn diagrams of contents and utility. They are often initially designed by a group for a specific need they have. They may have specific features that were terrific for some tasks. But they might not serve all the tasks or all the research needs in an area. It’s like RNA analysis: there are a number of ways to look at what the expression of a given RNA is: northerns, PCR, in situ hybridization, RNA-seq… And these each can do a piece of what you might need. But none of them gives all the answers alone.

So this week’s highlighted question is:

Question: What should I use blat for?

Is blat just general aligner like bwa or bowtie or does it have a niche application that it’s especially good at?


And the answer provide a lot of good detail about what it was designed for and how it compares to other tools. Users talk about the strengths and weaknesses of it for different reasons and tasks. It’s a nice example of the kinds of considerations to make when choosing to use a tool. Check out the discussion that ensues.