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.

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