TOPIC: Bioinformatics

Procedure:

1. D0 a BLAST search for the sequence in notepad file named: Blast Practice.
2. Perform a pairwise nucleotide sequence alignment of two sequences derived from the phenylalanine hydroxylase (PHA) gene using EMBOSS Water.
3. Perform a multiple sequence sequence alignment of three sequences derived from the VP1 genes of poliovirus using MUSCLE.
4. Analyze the results of each one

Question guides for discussion of Results:

1. BLAST Interpret the results:

• The query sequence belongs to what gene and organism?
• Is there any other organism with which it has similarity or differences?

2. Pairwise alignment:

? Look for gaps, differences in base composition, other relevant information

3. Multiple sequence alignment

?Discuss the differences among the input sequences. How many base differences do you see?

References:

\f>poliovirus1 VP1 cacattctta 1381 ttctgtggct caatgatggc aactggcaaa ttgttagtct cttatgcacc cccgggagca 1441 gacccaccca aaaagcgtaa agaagcgatg ttagggacac atgtaatctg ggatataggt 1501 ttacaatott cttgcaccat ggtggtaccg tggattagca acacaacata tagacagacc 1561 atagatgaca gotttaccga aggtggttac attagtgttt tctaccaaac cagaatagtg 1621 gtccccctct caacacctag ggaaatggac atcottgggt ttgtgtcggc atgcaacgat 1681 tttagcottc gottgotgcg agatactacc cacatagagc agaaagcatt atcacaggga 1741 ttggggcaga tgotggaaag tatgatagac aacactgttc gtgagacctc aagggcatca 1801 acatccaggg atgetctccc taacacagaa tccagcggac cggcacattc caaggaaatc 1861 cccgcactca ctgcagtaga ggcaggtgcc acgaacccat tggtcccttc agacactgtg 1921 caaactagac atgttattca gcacagatcg agatcagagt ctagtottga atcattcttc 1981 gcacgtggtg cttgtgtaac tattatgacc gtagataact cggcatccac cacgtccaaa >poliovirus2 VP1 1 ctatgccaca aggaattggt gacatgattg agggggccgt tgaagggatt actaaaaatg 61 cattggttcc cccgacttcc accaatagcc tgcctgacac aaagccgagc ggtccagccc 121 actccaagga gatacctgca ttgacagccg tggagacagg ggctaccaat ccgttggtgc 181 cttcggacac cotgcaaacg coccatgtca tccagagacg aacgcgatca gagtccacgg 241 ttgagtcatt ctttgcaaga ggggcttgcg tggctatcat tgaggtggac aatgatgcac 301 cgacaaagcg coccagcaga ttgttttcgg tttggaaaat aacttacaaa gatactgttc 361 aactgagacg caaactggaa tttttcacat attctagatt tgacatg >poliovirus3 VP1 1 gcgagacacc actcacattt cacaatctgc gottccacag ggtattgaag atttgatttc 61 tgaagttgca cagggcccc taactttgtc actcccgaag caacaggata gottacctga 121 tactaaggcc agtggcccgg cocattccaa ggaggtacct gcactcactg cagtcgagac 181 tggagccacc aatcctctgg caccatccga cacagttcaa acgcgccacg tagtccaacg 241 acgcagcagg tcagagtcca caatagaatc attcttcgca cgcggggcgt gcgtcgctat 301 tattgaggtg gacaatgaac aaccaaccac ccgggcacag aaactatttg ccatgtggcg 361 cattacatac aaagatacag tgcagttgcg ccgtaagttg gagtttttca catactctcg 421 ttttgacatg gaattca>BLAST practice CATAATGAATAGAAGGAAAAGATCTGTGACCATGCTCCTTATGCTGATGCC TACAGCCTTGGCGTTCCAT TTGACTACACGAGGGGGAGAGCCGCACATGATAGTCAGCAAGCAGGAAAGA GGAAAGTCACTCTTGTTTA AGACCTCAGCAGGTGTCAACATGTGCACCCTTATAGCGATGGATTTGGGAG AGTTATGTGAGGACACAAT GACTTACAAATGCCCTCGAATCACTGAAGCTGAACCAGATGACGTTGATTG TTGGTGCAATGCCACAGAC ACATGGGTGACCTATGGAACATGTTCCCAAACTGGCGAGCACCGACGAGAC AAACGTTCCGTCGCACTGG CCCCACACGTGGGACTTGGTTTGGAAACAAGAACCGAAACGTGGATGTCCT CTGAAGGCGCTTGGAAACA GATACAAAGAGTGGAGACTTGGGCCCTGAGACACCCAGGATTCACGGTGAT AGCCCTCTTTCTAGCACAT GCCATAGGAACATCCATCACTCAGAAAGGGATTATTTTCATTTTGTTAATG CTGGTAACACCATCCATGG CCATGCGATGCGTGGGAATAGGCAGCAGGGACTTCGTGGAAGGACTGTCAG GAGCAACCTGGGTAGATGT GGTACTGGAACATGGAAGTTGCGTCACCACCATGGCAAAAGACAAACCAAC ATTGGACATTGAACTCTTG AAGACGGAAGTCACAAACCCTGCCATCCTGCGCAAACTGTGCATTGAAGCT AAAATATCAAACACCACCA CCGACTCAAGATGTCCAACACAAGGAGAAGCCACACTGGTGGAAGAACAAG ACGCGAACTTTGTGTGTCG ACGAACGTTTGTGGACAGAGGCTGGGGCAATGGCTGTGGGCTCTTCGGAAA AGGAAGCTTAATAACGTGT GCTAAGTTCAAGTGTGTGACAAAACTGGAAGGAAAGATAGTTCAATATGAA AACTTGAAATATTCAGTAA TAGTTACCGTTCACACCGGAGACCAGCACCAGGTGGGAAATGAAAGCACAG AACATGGGACAACTGCAAC>NG 008690 . 2: 122822-123064 Homo sapiens phenylalanine hydroxylase (PAH ) , RefSeqGene on chromosome 12 GCCACTGAGAACTCTCTTAAGACTACCTTTCTCCAAATGGTGCCCTTCACT CAAGCCTGTGGTTTTGGTCTTAGGAACTT TGCTGCCACAATACCTCGGCCCTTCTCAGTTCGCTACGACCCATACACCCA AAGGATTGAGGTCTTGGACAATACCCAGC AGCTTAAGATTTTGGCTGATTCCATTAACAGTAAGTAATTTACACCTTACG AGGCCACTCGGTTTCTCAGTAATCGAAGA CTG