The3genesthatyouwillcompareatlistedbelow.doc

1. The 3 genes that you will compare at listed below. Take a look. I’ve colored ‘the header region’ of each so that you can distinguish one from the other.
DO NOT CHANGE THE FORMAT. DO NOT ADD TEXT OF ANY SORT. WHEN YOU COPY THE GENE DON’T FORGET TO INCLUDE THE ‘HEADER (RED) REGION (starting with “>”). The ‘>’ symbol tells the software the start of the gene. and the red region DESCRIBES THE GENE (SEQUENCE).

2. Using your computer, open the program (used to compare them). The link is
http://multalin.toulouse.inra.fr/multalin/
(cut and paste link into your browser)

3. Copy THE FIRST 2 SEQUENCES ONLY (1 and 2) and paste into the “white box-region” just below region marked Sequence-data. Make sure you copy the entire sequence for each gene including the ‘> symbol and red heading’.

4. Click the region below the box marked “Start MultiAlin’. This starts your comparison

5. Examine results. Make note of the colors. If the colors are ‘alike’ that means the sequences are similar.
THIS PROGRAM USES COLOR TO DETERMINE HOW SIMILAR 2 SEQUENCES ARE.

SAME COLOR MEANS THEY ARE SIMILAR.

6. Use the back-space button and return to the original screen. Delete the sequences in the white box. This allows for a new comparison.
7. Paste sequences 2 and 3 in the box. this allows for comparison of sequences 2 and 3, similar to what was done for 1 and 2.

8. Click the “Start MultiAlin” just like before.
9. Note the color- scheme. Compare what you observed for 1 and 2. Which are more similar 1 and 2, or 2 and 3?
10. For full credit, you should copy results from comparison of 1-2 and separately, 2-3. Doesn’t matter if you don’t have color printer.

11. Or… at the bottom of the image page, there is a command — “Results as a gif file’. It is located under the region marked, ‘AVAILABLE FILES’… Click on this (Results as a gif file’) and print your results. Staple the first comparison to the second, and turn in. or give as computer file. Which ever are more convenient? Tell me which 2 comparisons (ie, genes) are more alike.

COMPARISON SHOULD LOOK LIKE THIS… (red= exactly alike; blue = different sequence). I want you to take note of the sequences that red compared to those regions that are blue…)… the bottom = summary of the comparison- gene 1 versus 2) (more red= more alike)

There are 3 genes below… they start with the > symbol…
>gi|110623919|dbj|AK225484.1| Homo sapiens mRNA for growth arrest-specific 2 like 1 isoform a variant, clone: JTH00434

TCCAGTGAGGCCTACGTGGAGGCCATGAAGGAGGACCTGGCCGAGTGGCTCAATGCCTTGTACGGCCTGG

GTCTCCCGGGTGGTGGCGATGGCTTCCTGACAGGGCTGGCCACGGGCACGACCCTGTGCCAACATGCCAA

CGCCGTGACCGAGGCTGCCCGTGCATTGGCAGCCGCCCGCCCGGCCCGAGGTGTGGCCTTCCAGGCGCAC

AGTGTAGTGCCTGGCTCCTTCATGGCGCGCGACAACGTGGCCACCTTCATCGGCTGGTGCCGCGTGGAGC

TGGGTGTGCCGGAGGTGCTCATGTTTGAGACTGAGGACCTGGTGCTGCGCAAGAACGAGAAGAGCGTGGT

GCTGTGCCTGCTGGAGGTGGCGCGGCGTGGGGCACGCCTGGGCCTGCTGGCCCCACGCCTCGTGCAGTTT

GAGCAGGAGATTGAGCGGGAGCTGCGTGCTGCACCCCCAGCCCCCAACGCCCCTGCCGCTGGGGAGGACA

CCACTGAAACCGCCCCCGCACCAGGGACTCCTGCCCGCGGCCCCCGCATGACACCCAGCGACCTGCGCAA

CCTCGACGAGCTGGTGAGGGAGATTCTGGGCCGCTGCACCTGCCCTGACCAGTTTCCCATGATCAAGGTC

TCAGAGGGGAAGTACCGTGTGGGGGACTCGAGCCTGCTCATCTTTGTGCGGGTGCTGAGGAGCCACGTGA

TGGTGCGAGTGGGTGGTGGCTGGGACACGCTGGAGCATTACCTGGACAAGCACGACCCGTGCCGCTGCTC

CTCCACTGCTCATCGCCCACCCCAGCCGAGGGTCTGCACCTTTTCTCCACAGAGGGTGTCGCCCACCACC
>gi|21961309|gb|BC034582.1| Homo sapiens keratin associated protein 3-2, mRNA (cDNA clone MGC:34106 IMAGE:3909612), complete cds

CCTCATCTAAGAAACTGAAAGCTAACCAGACGCCCATTGCCATGGATTGCTGTGCCTCTCGCAGCTGCAG

TGTCCCCACTGGGCCTGCCACCACCATCTGCTCCTCCGACAAATCCTGCCGCTGTGGAGTCTGCCTGCCC

AGCACCTGCCCACACACAGTTTGGTTACTGGAGCCCATCTGCTGTGACAACTGTCCCCCACCCTGCCACA

TTCCTCAGCCCTGCGTGCCCACCTGCTTCCTGCTCAACTCCTGCCAGCCAACTCCGGGCCTGGAGACCCT

CAACCTCACCACCTTCACTCAGCCCTGCTGTGAGCCCTGCCTCCCAAGAGGCTGCTGATGGATGGCTACT

TTGCTCAGTGCCCGACAACGAAGAATCCAGAAGCTGTCCCTTCAGTATTCACTTGCCTCAGTAGTTTGCC

AGATGTTAAGGTAGACCAGATGACCCAGATATGAAGAACTTACCTTTGGTTTTAATGGGGGAAAAAAAGA

AAAGTATTTTTTATGGTTATTTAGCTGAAAAACCATTTGGTTCCTGTGGGCAGGTGAATGAGTTTTATTA

GCAAAATACTGTTTCAATCTTTAAGACCTCAGATTACATGTTCTTGATCATATTGCTTCCTGGCTCTTGT

TTCTTGTACTGGGTATTTTCATAGAAGAAAATTTCTTGGTGGGTTTTCCAATAAACTATATTTCTCTGGC

>gi|12655437|emb|AJ406932.1| Homo sapiens mRNA for keratin associated protein 5.3 (KRTAP 5.3 gene)

AAGAAACTGAAAGCTAACCAGACGCCCATTGCCATGGATTGCTGTGCCTCTCGCAGCTGCAGTGTCCCCA

CTGGGCCTGCCACCACCATCTGCTCCTCCGACAAATCCTGCCGCTGTGGAGTCTGCCTGCCCAGCACCTG

CCCACACACAGTTTGGTTACTGGAGCCCATCTGCTGTGACAACTGTCCCCCACCCTGCCACATTCCTCAG

CCCTGCGTGCCCACCTGCTTCCTGCTCAACTCCTGCCAGCCAACTCCGGGCCTGGAGACCCTCAACCTCA

ACATCCAGGCCGTGCGCACCCAGGAGAAGGAGCAGATCAAGACCCTCAACAACAAGTTTGCCTCCTTCAT

AGACAAGGTACGGTTCCTGGAGCAGCAGAACAAGATGCTGGAGACCAAGTGGAGCCTCCTGCAGCAGCAG

AGGTAGACCAGATGACCCAGATATGAAGAACTTACCTTTGGTTTTAATGGGGGAAAAAAAAGAAAAGTAT

TTTTTATGGTTATTTAGCTGAAAAACCATTTGGTTCCTGTGGGCAGGTGAATGAGTTTTATTAGCAAAAT

ACTGTTTCAATCTTTAAGACCTCAGATTCATGTTCTTGATCATATTGCTTCCTGGCTCTTGTTTCTTGTA

CTGGGTATTTTCATAGAAGAAAATTTCTTGGTGGGTTTTCCAATAAACTATATTTCTCTGGCAAAAAAAA