Bioinformatics Online Tutorial 4-2-3 PDF

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BIOINFORMATICS. On-Line Tutorial 4 Investigating the Human Genome and assembling DNA fragments to make contigs AIM. The aim of this investigation is to look at the NCBI map viewer see how much information we can find out about one gene. We also aim to assemble some sequences together to form a contig. Part 1. Human Genome Browsers Start by going to the NCBI homepage. 1.At the home page, click Genome on the right hand side. At the next page, follow the Human Genome link. 2.Search for the gene ENPEP. 3.What chromosome is this gene on? 4.What is the full name of this gene? 5.How many exons does it contain? Introns? What can you say about the relative size of introns to exons? 6.How many exons does the secondary transcript contain? 7.What is the function of the encoded protein? 8.What tissues is ENPEP mainly expressed in? 9.Click on the link to the mouse ortholog. If the gene structure similar? Is it encoded on the same chromosome as in humans? 10. If you scroll down, you can see the links to the mRNA and protein entries. 11. Click on the SNP: Geneview link. Describe the various forms on SNP’s found (what different types, rather than the actual changes). 12. Go back to the Human Genome home page. Search PAH. Re-answer the questions. 13. What chromosome is this gene on? 14. What is the full name of this gene? 15. How many exons does it contain? Introns? What can you say about the relative size of introns to exons? 16. How many exons does the secondary transcript contain? 17. What is the function of the encoded protein? 18. What tissues is ENPEP mainly expressed in? 19. Click on the link to the mouse ortholog. If the gene structure similar? Is it encoded on the same chromosome as in humans? If you scroll down, you can see the links to the mRNA and protein entries. 20. Click on the SNP: Geneview link. Describe the various forms on SNP’s found (what different types, rather than the actual changes). Part 2. Sequence assembly. The following sequence information is the sequence data obtained from a long range PCR, the sort of sequence information that would be used for filling in gaps between contigs. The sequences are in Fasta format. Paste them into the CAP3 assembly program to construct a contig

http://doua.prabi.fr/cgi-bin/run_cap3 Did all the sequences show some overlap? If no- which sequence(s) did not overlap to create a contig? Look at the assembly details file, and see if you can understand it! How many bp are there on the contig? >BPLF1 GCTCGACGGGTGACAGCTTCACCCTTATCAAGCTGGAAAACCAATTGAAGAGTTAGAACGAG AGCTAGGAATTACCAATATCATTAAGTTAGCATCCAATGAAAATCCATTTGGTTTGCCTGAC AGTGCTAAACAAGCGATTTTAGCGGAATTGGATAATCTGACGCGCTACCCTGACAGTAATGG CTTTTACTTTAAACAAACAGTCGCAAAAAAATTTGGCTTATCTCCTGAACAAATTACTTTAG GCAATGGTTCAAATGATTTATTAGAGTTAGTCGCGCATACCTTTGCTAATGAACAAGATGAA ATTCTCTTTTCACAATATGCCTTTATTGTGTATCCCCTTGTTACACAAGCGATCAATGCCAA AAAAGTGGAAATCCCAGCGAAAAACTATGGGGCTGATTTAGACGGTTTTTTACAGGCAATAA GTGATAAAACCAAATTAATTTATCTCGCGAACCCCAATAATCCGACAGGCACTTTTTTAAGT GCGGGTGAAATTTCCCAATTTTTAAATCAAGTGCCCGCGCATGTCATCGTGGTATTAGATGA GGCTTATACTGAATTTACCTTGCCGGAAGAGCGAGTAGATTCCTTTACGTTACTCAAAAAAC ACCCTAATCTTGTGATTTGTCGTACCCTTTCTAAAGCCTATGGTTTAGCGGGTTTGCGCATT GGTTACGCGGTTTCTTCTGCCGAGATTGCTGACCTCTTTAATCGCGTTCGCCAACCATTTAA CTGTAATAGTCTGGCATTAGCCGCTGCTACCGCGGTGCTGAATGATGATGCATTTATTGCGA AAGTGGCTGAAAACAACCGACAAGGGTTGAAGTTATTAGAAGACTTCTTTACAGCCAAAGGG TTTGAACTATATTCCTTCAAAGGCAATTTTGTCATGTTAGATGTCAATCAACCAGCCTTACC AATTTATCAGGCATTATTACAAAAAGGCGTGATTGTGCGTCCGATTGCAGGTTATGGCTACC CAAATCATTTACGGATAGCATCGGTTTACCAAGAAGAAACCAACGTTTTCTTACTCGCATTA GCGAAGTATTAAGGGCTTAAGCAAACTTATCCAGTGTATAGGAAATATAAACTCGGAATA >BPLF2 TGACGACTCCTTGCCGGAGAGCGAGTAGATTCCTTTACGTTACTCAAAAAACACCCTAATCT TGTGATTTGTCGTACCCTTTCTAAAGCCTATGGTTTAGCGGGTTTGCGCATTGGTTACGCGG TTTCTTCTGCCGAGATTGCTGACCTCTTTAATCGCGTTCGCCAACCATTTAACTGTAATAGT CTGGCATTAGCCGCTGCTACCGCGGTGCTGAATGATGATGCATTTATTGCGAAAGTGGCTGA AAACAACCGACAAGGGTTGAAGTTATTAGAAGACTTCTTTACAGCCAAAGGTTTGAACTATA TTCCTTCAAAAGGCAATTTTGTCATGTTAGATGTCAATCAACCAGCCTTACCAATTTATCAG GCATTATTACAAAAAGGCGTGATTGTGCGTCCGATTGCAGGTTATGGCTTACCAAATCATTT ACGGATTAGCATCGGTTTACCAGAAGAAAACCAACGTTTCTTACTCGCATTAAGCGAAGTAT TAGGGCTTTAAGCCAAACTTATCCAGTGTATAGGAAATATAAATCGTGATAAAAGATGCGAC CGCTATTACTCTCAATCCCATCAGTTATATTGAAGGCGAGGTGCGTTTACCGGGCTCCAAAA GCTTATCCAATCGCGCACTCTTACTTTCCGCATTAGCTAAAGGAAAAACAACATTAACCAAT CTGTTAGATAGTGATGATGTGCGCCATATGTTAAATGCGTTAAAAGAGCTTGGCGTGACTTA TCAACTGTCAGAAGACAAATCCGTCTGTGAAATTGAAGGCTTAGGACGTGCTTTTGAATGGC AAAGTGGCTTAGCTTTATTTTTGGGCAATGCAGGGACGGCGATGCGTCCCTTGACTGCCGCG CTTTGTTTATCGACACCGAAACAAGGAAGGCAAAAATGAAATAGTCTTGACTGGCGAACCTC GTATGGAAGAACGCCCAATACAACATTTTAGTTGAAGCATTATGTCAAGCTGGCGCAGAAAT TCAGTATTTAGAACAGAAAGGTTACCCACCTATCGCCATTCGAAAATCCGGACTCCAAGGGC GGACGAATACCAATTTGATG >BPLF3 GGCAGAGCTTGGCGTGACTTATCACTGTCAGAAGACAAATCCGTCTGTGAAATTGAAGGCTT AGGACGTGCTTTTGAATGGCAAAGTGGCTTAGCTTTATTTTTGGGCAATGCAGGGACGGCGA TGCGTCCCTTGACTGCCGCGCTTTGTTTATCGACACCGAACAAGGAAGGCAAAAATGAAATA GTCTTGACTGGCGAACCTCGTATGAAAGAACGCCCAATACAACATTTAGTTGAAGCATTATG TCAAGCTGGCGCAGAAATTCAGTATTTAGAACAAGAAGGTTACCCACCTATCGCCATTCGAA ATACCGGACTCAAAGGCGGACGAATACAAATTGATGGGTCAGTTTCTTCTCAATTTTTGACC GCACTTTTAATGGCAGCCCCGATGGCAGAGGCGGATACGGAAATTGAAATCATCGGTGAGCT GGTTTCCAAACCTTACATTGATCGATATGGATATGAACCATATTCCCGATGCAGCAATGACC

ATTGCCACCACAGCGCTTTTTGCAGAAGGTGAAACGGTCATTCGTAATATTTATAACTGGCG CGTAAAAGAAACTGATCGCTTGACCGCGATGGCGACCGAACTACGTAAGGTGGGGGCGGAAG TGGAAGAAGGCGAAGATTTTATTCGTATCCAGCCATTGAATCTAGCGCAATTTCAACATGCT GAAATTGAAACATACAATGATCACCGCATGGCGATGTGCTTTGCTTTAATCGCATTGTCGCA AACGTCGGTCACGATTTTAGACCCGAGCTGTACCGCAAAAACCTTTCCTACGTTTTTTGATA CTTTTTTACGCTTAACACACGCAGAAAGTTAGCCTACAGATAGGTACTAAGCAAAAAGCGAA GTATTTTGTAATACTTCGCTTTTTTGAGTGACGCATCGGGTCTGAGATAATGCAAGAAAACA CCCTTAGACTGAATCCGAAAACTCGCCATATAATTTGCGCTGACATCTTTATTGAGCCGAAT TTACCCGTCAATGGGATGGAATGATAAGCTACCATATCTAAACAGGTTAATTGGGCTTCATC ACACCAATGGAGGCATTCCCGCTGGCTTAA >BPLF4 GAAGGACTGGTTTCAACCTTACATTGATCGATATGGATATGAACCATATTCCCGATGCAGCA ATGACCATTGCCACCACAGCGCTTTTTGCAGAAGGTGAAACGGTCATTCGTAATATTTATAA CTGGCGCGTAAAAGAAACTGATCGCTTGACCGCGATGGCGACCGAACTACGTAAGGTGGGGG CGGAAGTGGAAGAAGGCGAAGATTTTATTCGTATCCAGCCATTGAATCTAGCGCAATTTCAA CATGCTGAAATTGAAACATACAATGATCACCGCATGGCGATGTGCTTTGCTTTAATCGCATT GTCGCAAACGTCGGTCACGATTTTAGACCCGAGCTGTACCGCAAAAACCTTTCCTACGTTTT TTGATACTTTTTTACGCTTAACACACGCAGAAAGTTAGCCTACAGATAGGTACTAAGCAAAA AGCGAAGTATTTTGTAATACTTCGCTTTTTGAGTGACGCATCGGGTCTGAGATAATGCAAGA AAACACCTTAAGACTGAATCCGAAAACTCGCCATATAATTTGCGCTGACATCTTTATTGAGC CAGAATTTACCCGTCAATGGATTGTAATGATAGCCTACCATATCTAAACAGGTTAATTGTGC TTCATCACACCAATGAAGCAATTCCGCTGGCTTAATAAATTTGTCGTAATCGTGCGTCCCTT TCGGCAACATTTTCAACACATATTCCGCACCAATAATCACCAATGCCCAGGCTTTAAGGGTT CGATTAATGGTGGAGAAAAAAATCACCCCGTTTGGTTTTAATAATTGCTTACAACAGGCAAT AATCGAACTCGGGTCAGGGCACATGCTCAAGCATTTCCATGCAAGTAATCACATCAAACTTT TCGTCCTCCCCTCTTTCAGCAAAAAGTGCGGTCTGATTTTGCAAAAATTCCTCAATCGTAAT TTGTTGATATCAATATGTAGCCCGCTTTCTAAAGCATGTTTCTTGCCACTTGTATGGGGCAG AAGACATATCAATCCCGGTCACAATTGCACCTTGCTTTGCCATGCTTTCTGACAAATGCCAC GCCACACCCACATCCAGCACTTTTTCCCGATAGCCCGTTGCCTGCTGGGCATATTAGCCTTA AACGTAACGGATAAGCTGGA >BPLR1 GTGGACCAAGTTTTTGGGGTTGACCTTTATCGAGGGCAACGATGTTAATGCCAAAAGTGACT TGCAATTGGGCCATTGCATACAAGTTGTTGAGAACCACTTCGCCCACGGCATCACGTTTGAT TTTAATTTCAATACGCATCCCGTCTTTGTCAGATAAATCCGTGATTGCGCTAATGCCTTCGA CTTTTTTCTCTTTTACGAGATCAGCAATTTTTTCGATTAATTTGGCTTTGTTGACTTGATAA GGAATTTCATGCACCACAATGGTTTCACCGCCTTTTTCATCGGTTTCCACTTCAGCTTTGGC ACGTACATAAATTTTACCACGTCCTGTTTTATAGGCTTCTTCAATCCCTTTGCGACCATTGA TTAATGCGGCGGTTGGGAAGTCTGGACCTGGAATATAAGTCATTAACTCATCAATGCTGATC TCGTTGTTTTCGATATACGCCAAACAACCGTCTAACACTTCGCCTAAGTTATGAGGGGGAAT ATTTGTTGCCATACCGACCGCAATACCGGAAGAACCGTTGACTAAAAGCGCAGGGACTTTGG TTGGGAGGACTTCAGGAATTTGTTCAGAGCCATCGTAGTTAGGCACAAAATTGACAGTTTCT TTATCGAGATCCGCTAATAATTCATGGGCGATTTTAGTCATACGGGCTTCAGTATAACGCAT TGCCGCGGCAGCATCGCCATCAATTGAACCGAAGTTACCTTGCCCATCTACTAACATATAAA CGTAATGAAAACGGCTGAGCC >BPLR2 TAATAACGTAATGAAAACGGCTGAGCCATGCGCACGAGTGTGTCATAGACCGCGCTATCACC ATGAGGGTGATACTTACCGATTACATCCCCTACGATACGAGCGGATTTACGATAAGGTTTGT TATAGGCATTCCCGCCTTCGTGCATCGCAAATAATACGCGGCGATGGACGGGTTTCAAACCA TCGCGTACATCGGGTAATGCACGCCCTACGATGACGGACATGGCATAATCGAGATATGAGGA TTTCAGCTCTTCTTCAATACTGATTGGGCTAATATCTTGATGCATAGTATCTTGGACTAAAT CGGTCATTGAAAACTTCCTAATCATTGAGTTTGATTAATCAAAAAATTGACGGAATTATAGC ATAAAATCTAGTGTTCCCCTAATTTTATAGTGAAATTTTGCCTGATTTGGGGAATAATAACG TATTGTTTCTATTCAAAATCATAAGAAGAAATTTCATGCAAAATATTGATCAACAAGAACTT GATAAGTTTGAGAAAATGGCAAAAAGCTGGTGGGATCCGCAAGGGGATTTCAAACCGATTCA TCAACTTAATCCGTTACGTTTAAGCTATATTGCACAGCAAGCCAACGGGCTAACGGGGAAAA AAGTGCTGGATGTGGGTTGTGGCGGTGGCATTTTGTCAGAAAGCATGGCAAAGCAAGGTGCA

ATTGTGACGGGGATTGATATGTCTTCTGCCCCATTACAAGTGGCAAGAAAACATGCTTTAGA AAGCGGGCTACATATTGATTATCAACAAATTACGATTGAGGAATTTTTGCAAAATCAGACCG CACTTTTTGCTGAAAGAGGGGAGGACGAAAAGTTTGATGTGATTACTTGCATGGAAATGCTT GAGCATGTGCCTGACCCGAGTTCGATTATTGCCTGTTGTAAGCAATATTAAAACCAAACGGG TGATTTTTTTTCTCCACCATTAATCGAACCCTTAAAGCCTGGGCATTGGTGATTATTGCTGC GGAATAATGTGTTGAAAAATGTTGCCCAAAGGGGACCGCACGA >BPLR3 GGCGTTGTCTTCTGACCATTACAGTGGCAAGAAAACATGCTTTAGAAAGCGGGCTACATATT GATTATCAACAAATTACGATTGAGGAATTTTTGCAAAATCAGACCGCACTTTTTGCTGAAAG AGGGGAGGACGAAAAGTTTGATGTGATTACTTGCATGGAAATGCTTGAGCATGTGCCTGACC CGAGTTCGATTATTGCCTGTTGTAAGCAATTATTAAAACCAAACGGGGTGATTTTTTTCTCC ACCATTAATCGAACCCTTAAAGCCTGGGCATTGGTGATTATTGGTGCGGAATATGTGTTGAA AATGTTGCCGAAAGGGACGCACGATTACGACAAATTTATTAAGCCAGCGGAATTGCTTCATT GGTGTGATGAAGCACAATTAACCTGTTTAGATATGGTAGGCTATCATTACAATCCATTGACG GGTAAATTCTGGCTCAATAAAGATGTCAGCGCAAATTATATGGCGAGTTTTCGGATTCAGTC TTAAGGTGTTTTCTTGCATTATCTCAGACCCGATGCGTCACTCAAAAAGCGAAGTATTACAA AATACTTCGCTTTTTGCTTAGTACCTATCTGTAGGCTAACTTTCTGCGTGTGTTAAGCGTAA AAAAGTATCACAAAACGTAGGAAAGGTTTTTGCGGTACAGCTCGGGTCTAAAATCGTGACCG ACGTTTGCGACAATGCGATTAAAGCAAAGCACATCGCCATGCGGTGATCATTGTATGTTTCA ATTTCAGCATGTTGAAATTGCGCTAGATTCAATGGCTGGATACGAATAAAATCTTCGCCTTC TTCCACTTCCGCCCCCACCTTACGTAGTTCGGTCGCCATCGCGGTCAAGCGATCAGTTTCTT TTACGCGCCAGTTATAAAATATTACGAAATGACCGTTTCACCTTTCTGCAAAAAGCGCTGTG GGTGGGCAATGGTCATTTGCTTGCATCGGGAAT >BPLR4 CAAAAGCAAGCACATCGCCATGCGGTGATCATTGTATGTTTCAATTTCAGCATGTTGAAATT GCGCTAGATTCAATGGCTGGATACGAATAAAATCTTCGCCTTCTTCCACTTCCGCCCCCACC TTACGTAGTTCGGTCGCCATCGCGGTCAAGCGATCAGTTTCTTTTACGCGCCAGTTATAAAT ATTACGAATGACCGTTTCACCTTCTGCAAAAAGCGCTGTGGTGGCAATGGTCATTGCTGCAT CGGGAATATGGTTCATATCCATATCGATCAATGTAAGGTTTGGAAACCAGCTCACCGATGAT TTCAATTTCCGTATCCGCCTCTGCCATCGGGGCTGCCATTAAAAGTGCGGTCAAAAATTGAG AAGAAACTGACCCATCAATTTGTATTCGTCCGCCTTTGAGTCCGGTATTTCGAATGGCGATA GGTGGGTAACCTTCTTGTTCTAAATACTGAATTTCTGCGCCAGCTTGACATAATGCTTCAAC TAAATGTTGTATTGGGCGTTCTTTCATACGAGGTTCGCCAGTCAAGACTATTTCATTTTTGC CTTCCTTGTTCGGTGTCGATAAACAAAGCGCGGCAGTCAAGGGACGCATCGCCGTCCCTGCA TTGCCCAAAAATAAAGCTAAGCCACTTTGCCATTCAAAAGCACGTCCTAAGCCTTCAATTTC ACAGACGGATTTGTCTTCTGACAGTTGATAAGTCACGCCAAGCTCTTTTAACGCATTTAACA TATGGCGCACATCATCACTATCTAACAGATTGGTTAATGTTGTTTTTCCTTTAGCTAATGCG GAAAGTAAGAGTGCGCGATTGGATAAGCTTTTGGAGCCCGGTAAACGCACCTCGCCTTCAAT ATAACTGATGGGATTGAGAGTAATAGCGGTCGCATCTTTTATCACGATTTATATTTCCTATA CACTGGATAAGTTTGGCTTAAAGCCCTTAATACTTCGCTTAATGCGAGTAAGAAACGTTGGT TTTCTTCTGGTAAACCGATGCTAATCCGGAATGATTTGGTAAGGCATACCTGCAATCCGACC GCACATCCCGCCCTTTTTGTAATAATGCCTGATAATTGTTAAGGCTGGTTGATTGACTCCTA CATGAACAAATTTGCTTTTTGAAGAAATTAGTTTCAAACCTTTGGCCTGTA...