Bioinformatics tools

These are online tools that are helpfull to compare the DNA an dprotein codes of organisms.

BLAST
BLAST stands for Basic Local Alignment Search Tool.

see the article for more information.

Let me show you how to do it, you don't have to be a scientists to compare DNA.


 * The Cretaceous Weevil DNA sequence is number L08072 on GenBank.
 * Go to blast.ncbi.nlm.nih.gov. On this website you can compare ANY DNA, RNA or protein sequence with ALL KNOWN sequences.
 * We want to compare DNA sequences, so click on nucleotide blast.
 * It says "Enter accession number(s), gi(s), or FASTA sequence(s)"
 * Enter L08072 (the number in GenBank)
 * We want to compare the Weevil sequence with ALL known DNA sequences. So, don't change the settings.
 * Scroll down and hit BLAST.
 * Allignments are made in a few seconds.
 * Scroll down to Sequences producing significant alignments:
 * Here there is a list with all the matches found.

The first column gives the number and species of the DNA sequence, the Max ident column shows how many % the sequences are identical. Lets summarize what we see:

Multiple sequence alignment
This tool puts the sequences of multiple organism in rows beneath each other. Moreover it makes sure that identical regions are precisely beneath each other.

see for more information.

One tool to do this is Clustal Omega. This is how it works:


 * Go to Clustal Omega
 * STEP 1 - Enter your input sequences
 * In our case we're gonna compare proteins, so set it on PROTEINS
 * We are not gonna use the large empty space.
 * We will upload a Notepad file containing the sequences.
 * We will compare the dinosaur Collagen alpha-1(I) chain with some birds
 * Tyrannosaur sequence
 * click on the top on FASTA
 * copy-paste everything from ">gi" to the bottom into a Notepad file.
 * Go two rows further in Notepad.
 * Copy-paste in this file also the FASTA sequences of these organisms:
 * Brachylophosaurus
 * Anolis carolinensis
 * Chicken
 * Mammoth
 * rat
 * Add more if you like
 * Save your notepad
 * Upload the notepad file
 * Scroll down and hit SUBMIT
 * Wait a moment
 * Here you see that all sequences are aligned
 * Click on SHOW COLORS to make the graph even better.