Online Tools


Text Fragmenter for modeling how fragmented sequences can be resassembled using overlapping regions.
(For more control over the model, use this version, which has options to change the read size and include index sequences.)

vcf to FASTA converter for use in our online Mutations Investigation Experiment module.


Basic Local Alignment Search Tool (BLAST) searches NCBI databases for nucleotide or protein sequences which match the search query.(For practice using BLAST use our activity.)

Clustal Omega multiple sequence alignment (>2 samples) for protein, RNA, or DNA sequecnes. Used to generate a percent similarity matrix in our genetics of race module.

EMBOSS needle protein or nucleotide pairwise alignment (2 samples) for protein and nucleotide sequences.

ExPASy translates a given nucleotide for every reading frame and highlights potential proteins.

iCn3D 3D protein viewer. Use "File > Retrieve by ID" to bring up protein by protein database or pubchem identifiers.

Online Resources


NCBI databases collection of databases from the National Center for Biotechnology Information.

EBI Metagenomics collection of metagenomic data from a variety of biomes.

RCSB Protein Data Bank protein database which includes structure models.


A lot of bioinformatics tools exist for working with sequencing data. Here's a list of the free, online tools and resources we've either generated or found for use in our modules.