Online tools for biologists

If you do cloning work, you will probably need to add these tools to your bookmarks. I recommend creating a folder for these if you use a bookmark toolbar. Write us or drop a comment if your favorite tool is missing from the list.

NCBI BLAST

The Basic Local Alignment Search Tool (BLAST) at the NCBI website is perhaps the most popular online destination for molecular biologists. With BLAST you can compare your sequence to database sequences so you can find regions of similarity. Click here to go to BLAST.

ClustalW2

Hosted at the European Bioinformatics Institute website, ClustalW2 is a sequence alignment program useful when you have a number of sequences and you want to, well, align them to find regions of similarity. Unlike BLAST, with ClustalW2 you are comparing your own sequences, not your sequence against a database.

ExPASy Translate tool

Translates your nucleotide sequence into a protein sequence. Visit ExPASy.

Reverse Translate

If you have a protein sequence and you want to reverse translate it to the nucleotide sequence, Reverse Translate is your tool.

Reverse Compliment

This comes in handy when you are designing primers. Reverse Compliment does as its name suggest – it reverses your sequence and compliments it. You can also change settings if you only want to reverse without complimenting or to compliment without reversing. It is a nice bookmark for researchers.

Reverse Translate and Reverse Compliment are hosted at bioinformatics.org

NEBcutter

This is a handy tool for cloning work. NEBcutter allows you to check for restriction enzymes that cut your sequence only once. You can “custom digest” your sequence to check if specific restiction sites exist on your sequence.  Worth mentioning while we are at NEB is their Double Digest Finder, which allows you to check if the two restriction enzymes you will be using can actually work together in a double digestion (in my defense, English is my second language).

OligoAnalyzer

From Integrated DNA Technologies, OligoAnalyzer analyzes your primers for Tm, hairpins, self-dimers etc.

Primer3

This is your primer design tool for picking primers from a DNA sequence. The website is rather cluttered but the tool is nifty enough.