Free Molecular Biology Tools on the Web

Free Molecular Biology Tools on the Web A tutorial in 8 easy steps

The following is a nucleotide sequence for a gene pulled from GenBank (reference on a later page � no cheating!). I have modified it slightly, because nature is not normally so kind as to supply you with exactly what you need, so you�ll have to work a little bit to get to where we�re going.

Your job in this tutorial will be:

Determine just what the heck this sequence is encoding
Characterize it with a couple of different web tools to confirm it
Find similar sequences
Align them to find conserved and variable regions
Make a tree of your sequences

Step 1: FASTA Format

FASTA format is the standard format for most every molecular biology application. It consists of an initial descriptor line starting with a �>� followed by a sequence of nucleotides or peptides. Follow the instructions below to turn this sequence into FASTA format.

ATTTACGCGAAGCTCTTCGCAAAACCTTCGACCACCGACTTCAGCTTGGCAGCGGTGTCGTCGGAGAGGTCGCGGC TGTCGCGGATCGAATTGAGGATCTCGACGTTCTTGCCGCGCAGCAGCGAGAGCAGACCGTCCTCGAACGCGCGCAC CTTGTTAACGGGGAGCGGATCGAGATAGCCGTTGGTGCCAGCCCAGATCACGCAGACCTGCTCTTCCATCTTCAGC GGCGAGAACTGCGGCTGCTTCAGGAGCTCGGTCAGGCGCGAACCGCGGTTGAGCAGGCGCTGGGTCGAGGCGTCGA GGTCGGAGCCGAACTGCGCGAACGCCGCCATTTCGCGATACTGCGCGAGCTCGCCCTTGATCTTGCCGGCGACCTT CTTGGTGGCCTTGGTCTGCGCGGACGAACCGACGCGCGACACCGACAGACCGACGTTCACCGCGGGACGGATTCCC TGGAAGAACAGGTCGGTTTCCAGGAAGATCTGGCCGTCGGTGATCGAGATGACGTTGGTCGGGATGTAGGCCGACA CGTCGTTGGCCTGGGTTTCGATAATAGGCAGCGCAGTCAGCGAGCCCGAGCCATGATCCTTGCTGAGCTTCGCCGC GCGCTCGAGCAGGCGGGAGTGCAGATAGAACACGTCGCCCGGATAGGCTTCGCGGCCCGGCGGACGGCGCAGCAGC AGCGACATCTGGCGGTAAGCGACGGCCTGCTTGGACAGATCGTCATAGATGATGACGGCGTGCATGCCGTTATCGC GGAAGAATTCGCCCATGGTGCAGGCAGTAAAGGGGGCAATGTACTGCATCGGCGCCGGATCCGAGGCGGTGGCGGC GACGATGATCGAGTATTCGAGCGCGCCCTGCTCTTCCAGCACCTTCACGAACTGGGCGACGGTCGAACGCTTCTGG CCGACTGCGACGTAGACGCAGTACAGCTTGATGTTCTCGTCGGGCTGCGCGTTGAGCGGCTTCTGGTTCAGGATGG TGTCGAGCGCGATCGCGGTCTTGCCGGTCTGACGGTCGCCGATGATCAGCTCGCGCTGGCCGCGGCCGATCGGGAT CAGGGCGTCGATCGCCTTGAGGCCGGTCGCCATCGGCTCGCTCACCGACTTGCGCGGAATGATGCCGGGCGCCTTG ACGTCGACGCGCATACGCTTGTCGGCCTGGATCGGGCCCTTGCCGTCGATCGGGTTGCCGAGCGCGTCGACGACGC GGCCGAGCAGGCCCTTGCCGACCGGCGCGTCCACGATGGCGCGGGTGCGCTTGACGGTCTGACCTTCCTTGATCTC GCGGTCGGCACCGAAAATAACGACGCCGACGTTGTCGGTTTCGAGGTTCAGCGCCATGCCGCGGGTGCCGTTCTCG AACTCGACCATCTCACCGGCCTGGACGTTGTCCAGACCGTAGACGCGGGCGATACCGTCGCCGACGGACAGCACCT GTCCGACTTCGGAGACTTCAGCTTCCTGGCCGAAATTCTTGATCTGGTCCTTGAGGATCGCGGAAATTTCCGCGGC
GCGGATGTCCATTTUTAT

Open Windows Notepad. Notepad is the best friend of anyone working with sequences.
Cut and paste the above sequence into Notepad.
Before the first letter of the sequence, use Enter to create an empty line.
In that empty line, insert a > followed by a line describing the sequence.
Your file, now in FASTA format, should look something like this:

>Unknown Tutorial Sequence #1
ATTTACGCGAAGCTCTTCGCAAAACCTTCGACCACCGACTTCAGCTTGGCAGCGGTGTCGTCGGAGAGGTCGCGGC TGTCGCGGATCGAATTGAGGATCTCGACGTTCTTGCCGCGCAGCAGCGAGAGCAGACCGTCCTCGAACGCGCGCAC CTTGTTAACGGGGAGCGGATCGAGATAGCCGTTGGTGCCAGCCCAGATCACGCAGACCTGCTCTTCCATCTTCAGC GGCGAGAACTGCGGCTGCTTCAGGAGCTCGGTCAGGCGCGAACCGCGGTTGAGCAGGCGCTGGGTCGAGGCGTCGA GGTCGGAGCCGAACTGCGCGAACGCCGCCATTTCGCGATACTGCGCGAGCTCGCCCTTGATCTTGCCGGCGACCTT CTTGGTGGCCTTGGTCTGCGCGGACGAACCGACGCGCGACACCGACAGACCGACGTTCACCGCGGGACGGATTCCC TGGAAGAACAGGTCGGTTTCCAGGAAGATCTGGCCGTCGGTGATCGAGATGACGTTGGTCGGGATGTAGGCCGACA CGTCGTTGGCCTGGGTTTCGATAATAGGCAGCGCAGTCAGCGAGCCCGAGCCATGATCCTTGCTGAGCTTCGCCGC GCGCTCGAGCAGGCGGGAGTGCAGATAGAACACGTCGCCCGGATAGGCTTCGCGGCCCGGCGGACGGCGCAGCAGC AGCGACATCTGGCGGTAAGCGACGGCCTGCTTGGACAGATCGTCATAGATGATGACGGCGTGCATGCCGTTATCGC GGAAGAATTCGCCCATGGTGCAGGCAGTAAAGGGGGCAATGTACTGCATCGGCGCCGGATCCGAGGCGGTGGCGGC GACGATGATCGAGTATTCGAGCGCGCCCTGCTCTTCCAGCACCTTCACGAACTGGGCGACGGTCGAACGCTTCTGG CCGACTGCGACGTAGACGCAGTACAGCTTGATGTTCTCGTCGGGCTGCGCGTTGAGCGGCTTCTGGTTCAGGATGG TGTCGAGCGCGATCGCGGTCTTGCCGGTCTGACGGTCGCCGATGATCAGCTCGCGCTGGCCGCGGCCGATCGGGAT CAGGGCGTCGATCGCCTTGAGGCCGGTCGCCATCGGCTCGCTCACCGACTTGCGCGGAATGATGCCGGGCGCCTTG ACGTCGACGCGCATACGCTTGTCGGCCTGGATCGGGCCCTTGCCGTCGATCGGGTTGCCGAGCGCGTCGACGACGC GGCCGAGCAGGCCCTTGCCGACCGGCGCGTCCACGATGGCGCGGGTGCGCTTGACGGTCTGACCTTCCTTGATCTC GCGGTCGGCACCGAAAATAACGACGCCGACGTTGTCGGTTTCGAGGTTCAGCGCCATGCCGCGGGTGCCGTTCTCG AACTCGACCATCTCACCGGCCTGGACGTTGTCCAGACCGTAGACGCGGGCGATACCGTCGCCGACGGACAGCACCT GTCCGACTTCGGAGACTTCAGCTTCCTGGCCGAAATTCTTGATCTGGTCCTTGAGGATCGCGGAAATTTCCGCGGC
GCGGATGTCCATTTUTAT

If it does, proceed on to the next page.

Home Page

Hosted by www.Geocities.ws