DNA Structure 33 “ Sense” strand 5 “ Anti-sense strand Convention Sense strand Read5÷3 Reverse Complement
DNA structure 5’ 3’ 3’ 5’ “Sense” strand “Anti-Sense” strand Convention: Sense strand Read 5’Æ 3’ Reverse Complement
Genetics experiment Isolate a yeat mutant that has increased chromosome number phenotype Can rescue the phenotype with a piece of DNA corresponds to a site of mutation in the yeasts DNA genotype CGTTTTTCCTGTAAAGCGCTTAATTTGTTTACCATTCTATAAAAACCTTGAGCTAAGGCCAACTGATGCA ATTGCTCAAGTGAATGCATAAACAAAGCAAGATCATTCTTAGCGCAAAAAAAACTGGGATTTTGAAATAC AACAAAAGAAAGAAGTAAAAAGGGAATGCAACGCAATAGTTTAGTAAATATCAAACTAAACGCTAATTCG CCATCGAAAAAGACCACAACAAGACCAAATACGTCCAGGATCAATAAACCATGGAGAATATCCCATTCGC CGCAGCAAAGAAACCCGAATTCAAAAATACCTTCACCTGTAAGAGAAAAATTGAACAGATTACCTGTAAA CAATAAGAAGTTTTTGGATATGGAAAGCTCCAAAATTCCATCACCTATAAGGAAAGCGACTTCTTCCAAA ATGATACACGAAAATAAGAAGCTACCTAAATTTAAATCCCTATCACTCGATGACTTTGAACTGGGGAAGA AATTAGGAAAGGGTAAATTCGGTAAAGTTTATTGCGTTCGGCACAGGAGTACAGGATATATTTGCGCACT GAAAGTAATGGAGAAGGAAGAAATAATAAAGTATAATTTACAGAAACAATTCAGAAGGGAGGTAGAAATA CAAACATCGCTAAATCATCCGAATCTAACTAAATCATACGGCTATTTTCATGATGAAAAAAGAGTGTACC TGCTAATGGAATACTTAGTCAATGGGGAAATGTATAAACTATTGAGGTTACACGGACCCTTCAACGATAT TTTAGCATCAGATTATATTTATCAAATTGCCAATGCCCTAGATTATATGCATAAAAAGAATATTATTCAT AGAGATATTAAACCTGAAAATATACTAATAGGGTTCAATAATGTCATTAAGTTAACGGACTTCGGATGGA GTATAATAAATCCGCCAGAAAATAGAAGGAAAACTGTCTGTGGGACAATTGACTACCTTTCTCCAGAAAT GGTGGAGTCAAGGGAATATGATCACACTATAGATGCATGGGCTCTTGGCGTCCTGGCGTTTGAACTACTG ACCGGTGCCCCTCCGTTCGAAGAAGAAATGAAAGATACTACATATAAAAGGATAGCAGCACTGGATATCA AAATGCCCAGTAACATTTCTCAGGATGCGCAAGATTTAATACTTAAACTACTAAAATACGACCCCAAAGA TAGAATGCGCCTTGGAGACGTAAAAATGCATCCTTGGATACTAAGAAACAAGCCCTTTTGGGAAAATAAG CGGTTATAGAATTAAAGTATGACAGAATCGTTTGAAGGGCACTATTAATCACTCCCGCACATATCACATA ATACTAAGTATCCATTTCTAATATTTCATTACTCTTTTCGGCATCGTATATTGCGATATTTGATTAAATT TTCTTGTTCATTTTTTCCTCTTTTCTTTCGCCTTTGTCGAAAGAAAAGAGGAAAACAAGCTGAAAATTGC TATGCATTAAAGTAGCAGATTTACTTTGTTGAGTTGGTTCTGATCAATAATAAGAGTAATGAAAGAAAGC AAAAAAATGGCTAAAGATAATTTAACTAATTTGCTCTCTCAATTGAACATTCAATTGTCTCAA
Genetics experiment: phenotype Isolate a yeat mutant that has increased chromosome number Can rescue the phenotype with a piece of DNA …corresponds to a site of mutation in the yeasts DNA genotype CGTTTTTCCTGTAAAGCGCTTAATTTGTTTACCATTCTATAAAAACCTTGAGCTAAGGCCAACTGATGCA ATTGCTCAAGTGAATGCATAAACAAAGCAAGATCATTCTTAGCGCAAAAAAAACTGGGATTTTGAAATAC AACAAAAGAAAGAAGTAAAAAGGGAATGCAACGCAATAGTTTAGTAAATATCAAACTAAACGCTAATTCG CCATCGAAAAAGACCACAACAAGACCAAATACGTCCAGGATCAATAAACCATGGAGAATATCCCATTCGC CGCAGCAAAGAAACCCGAATTCAAAAATACCTTCACCTGTAAGAGAAAAATTGAACAGATTACCTGTAAA CAATAAGAAGTTTTTGGATATGGAAAGCTCCAAAATTCCATCACCTATAAGGAAAGCGACTTCTTCCAAA ATGATACACGAAAATAAGAAGCTACCTAAATTTAAATCCCTATCACTCGATGACTTTGAACTGGGGAAGA AATTAGGAAAGGGTAAATTCGGTAAAGTTTATTGCGTTCGGCACAGGAGTACAGGATATATTTGCGCACT GAAAGTAATGGAGAAGGAAGAAATAATAAAGTATAATTTACAGAAACAATTCAGAAGGGAGGTAGAAATA CAAACATCGCTAAATCATCCGAATCTAACTAAATCATACGGCTATTTTCATGATGAAAAAAGAGTGTACC TGCTAATGGAATACTTAGTCAATGGGGAAATGTATAAACTATTGAGGTTACACGGACCCTTCAACGATAT TTTAGCATCAGATTATATTTATCAAATTGCCAATGCCCTAGATTATATGCATAAAAAGAATATTATTCAT AGAGATATTAAACCTGAAAATATACTAATAGGGTTCAATAATGTCATTAAGTTAACGGACTTCGGATGGA GTATAATAAATCCGCCAGAAAATAGAAGGAAAACTGTCTGTGGGACAATTGACTACCTTTCTCCAGAAAT GGTGGAGTCAAGGGAATATGATCACACTATAGATGCATGGGCTCTTGGCGTCCTGGCGTTTGAACTACTG ACCGGTGCCCCTCCGTTCGAAGAAGAAATGAAAGATACTACATATAAAAGGATAGCAGCACTGGATATCA AAATGCCCAGTAACATTTCTCAGGATGCGCAAGATTTAATACTTAAACTACTAAAATACGACCCCAAAGA TAGAATGCGCCTTGGAGACGTAAAAATGCATCCTTGGATACTAAGAAACAAGCCCTTTTGGGAAAATAAG CGGTTATAGAATTAAAGTATGACAGAATCGTTTGAAGGGCACTATTAATCACTCCCGCACATATCACATA ATACTAAGTATCCATTTCTAATATTTCATTACTCTTTTCGGCATCGTATATTGCGATATTTGATTAAATT TTCTTGTTCATTTTTTCCTCTTTTCTTTCGCCTTTGTCGAAAGAAAAGAGGAAAACAAGCTGAAAATTGC TATGCATTAAAGTAGCAGATTTACTTTGTTGAGTTGGTTCTGATCAATAATAAGAGTAATGAAAGAAAGC AAAAAAATGGCTAAAGATAATTTAACTAATTTGCTCTCTCAATTGAACATTCAATTGTCTCAA
The national Center for Biotechnology Information Created as a part of nlm in 1988 Establish public databases Perform research in computational biology Develop software tools for sequence analysis Disseminate biomedical information
The National Center for Biotechnology Information • Created as a part of NLM in 1988 – Establish public databases – Perform research in computational biology – Develop software tools for sequence analysis – Disseminate biomedical information
Molecular databases Primary Databases Original submissions by experimentalists Database staff organize but don't add additional information Example: Gen Bank · Derivative databases Human curated compilation and correction of data Example: SWISS-PROT, NCBI Refseq mRNA Computationally Derived Example: UniGene Combinations Example: NCBI Genome Assembly
Molecular Databases • – – information • • – • • – • – • Primary Databases Original submissions by experimentalists Database staff organize but don’t add additional Example: GenBank Derivative Databases Human curated compilation and correction of data Example: SWISS-PROT, NCBI RefSeq mRNA Computationally Derived Example: UniGene Combinations Example: NCBI Genome Assembly
What is Gen Bank? NCBl's Primary sequence Database Nucleotide only sequence database · Archival in nature Gen Bank Data Direct submissions individual records BankIt, Sequin) Batch submissions via email ( EST, GSS, STs ftp accounts sequencing centers Data shared three collaborating databases Gen Bank DNA Database of Japan(DDBJ) European Molecular Biology Laboratory Database (EMB凵) at Ebl
What is GenBank? • Nucleotide only sequence database • Archival in nature • – Direct submissions individual records (BankIt, Sequin) – Batch submissions via email (EST, GSS, STS) – ftp accounts sequencing centers • Data shared three collaborating databases – GenBank – DNA Database of Japan (DDBJ). – (EMBL) at EBI. NCBI’s Primary Sequence Database GenBank Data European Molecular Biology Laboratory Database