Lab 2 - NCBI Tools, Pairwise Sequence Alignment and Analysis Answer Key | BCB 444, Lab Reports of Bioinformatics

Download Lab 2 - NCBI Tools, Pairwise Sequence Alignment and Analysis Answer Key | BCB 444 and more Lab Reports Bioinformatics in PDF only on Docsity! BCB 444/544 Lab 2 – NCBI Tools, Pairwise Sequence Alignment & Analysis Answer Key 30 points possible. Score converted to 10 pt. scale, rounded to nearest tenth. 1 pt. 1. a) Entrez allows text-based searches of all NCBI databases. It can be used to search for nucleotides, proteins, and structures, as well as organism taxonomy and genome features. Biological and genetics publications are also searched. For instance, a user can retrieve sequence data for a particular group of organisms, or find articles related to apoptosis. 1 pt. b) 509 1 pt. c) 37 1 pt. f) 33,455 1 pt. g) 9 1 pt. i) >gi|5031767|ref|NP_005517.1| heat shock transcription factor 1 [Homo sapiens] MDLPVGPGAAGPSNVPAFLTKLWTLVSDPDTDALICWSPSGNSFHVFDQGQFAKEVLPKYFKHNNMASFV RQLNMYGFRKVVHIEQGGLVKPERDDTEFQHPCFLRGQEQLLENIKRKVTSVSTLKSEDIKIRQDSVTKL LTDVQLMKGKQECMDSKLLAMKHENEALWREVASLRQKHAQQQKVVNKLIQFLISLVQSNRILGVKRKIP LMLNDSGSAHSMPKYSRQFSLEHVHGSGPYSAPSPAYSSSSLYAPDAVASSGPIISDITELAPASPMASP GGSIDERPLSSSPLVRVKEEPPSPPQSPRVEEASPGRPSSVDTLLSPTALIDSILRESEPAPASVTALTD ARGHTDTEGRPPSPPPTSTPEKCLSVACLDKNELSDHLDAMDSNLDNLQTMLSSHGFSVDTSALLDLFSP SVTVPDMSLPDLDSSLASIQELLSPQEPPRPPEAENSSPDSGKQLVHYTAQPLFLLDPGSVDTGSNDLPV LFELGEGSYFSEGDGFAEDPTISLLTGSEPPKAKDPTVS Note: credit was given as long as the top two lines were present 1 pt. j) >gi|132626772|ref|NM_005526.2| Homo sapiens heat shock transcription factor 1 (HSF1), mRNA GCGGCGGGAGCGCGCCCGTTGCAAGATGGCGGCGGCCATGCTGGGCCCCGGGGCTGTGTGTGCGCAGCGG GCGGCGGCGCGGCCCGGAAGGCTGGCGCGGCGACGGCGTTAGCCCGGCCCTCGGCCCCTCTTTGCGGCCG CTCCCTCCGCCTATTCCCTCCTTGCTCGAGATGGATCTGCCCGTGGGCCCCGGCGCGGCGGGGCCCAGCA ACGTCCCGGCCTTCCTGACCAAGCTGTGGACCCTCGTGAGCGACCCGGACACCGACGCGCTCATCTGCTG GAGCCCGAGCGGGAACAGCTTCCACGTGTTCGACCAGGGCCAGTTTGCCAAGGAGGTGCTGCCCAAGTAC TTCAAGCACAACAACATGGCCAGCTTCGTGCGGCAGCTCAACATGTATGGCTTCCGGAAAGTGGTCCACA TCGAGCAGGGCGGCCTGGTCAAGCCAGAGAGAGACGACACGGAGTTCCAGCACCCATGCTTCCTGCGTGG CCAGGAGCAGCTCCTTGAGAACATCAAGAGGAAAGTGACCAGTGTGTCCACCCTGAAGAGTGAAGACATA AAGATCCGCCAGGACAGCGTCACCAAGCTGCTGACGGACGTGCAGCTGATGAAGGGGAAGCAGGAGTGCA TGGACTCCAAGCTCCTGGCCATGAAGCATGAGAATGAGGCTCTGTGGCGGGAGGTGGCCAGCCTTCGGCA GAAGCATGCCCAGCAACAGAAAGTCGTCAACAAGCTCATTCAGTTCCTGATCTCACTGGTGCAGTCAAAC CGGATCCTGGGGGTGAAGAGAAAGATCCCCCTGATGCTGAACGACAGTGGCTCAGCACATTCCATGCCCA AGTATAGCCGGCAGTTCTCCCTGGAGCACGTCCACGGCTCGGGCCCCTACTCGGCCCCCTCCCCAGCCTA CAGCAGCTCCAGCCTCTACGCCCCTGATGCTGTGGCCAGCTCTGGACCCATCATCTCCGACATCACCGAG CTGGCTCCTGCCAGCCCCATGGCCTCCCCCGGCGGGAGCATAGACGAGAGGCCCCTATCCAGCAGCCCCC TGGTGCGTGTCAAGGAGGAGCCCCCCAGCCCGCCTCAGAGCCCCCGGGTAGAGGAGGCGAGTCCCGGGCG CCCATCTTCCGTGGACACCCTCTTGTCCCCGACCGCCCTCATTGACTCCATCCTGCGGGAGAGTGAACCT GCCCCCGCCTCCGTCACAGCCCTCACGGACGCCAGGGGCCACACGGACACCGAGGGCCGGCCTCCCTCCC CCCCGCCCACCTCCACCCCTGAAAAGTGCCTCAGCGTAGCCTGCCTGGACAAGAATGAGCTCAGTGACCA CTTGGATGCTATGGACTCCAACCTGGATAACCTGCAGACCATGCTGAGCAGCCACGGCTTCAGCGTGGAC ACCAGTGCCCTGCTGGACCTGTTCAGCCCCTCGGTGACCGTGCCCGACATGAGCCTGCCTGACCTTGACA GCAGCCTGGCCAGTATCCAAGAGCTCCTGTCTCCCCAGGAGCCCCCCAGGCCTCCCGAGGCAGAGAACAG CAGCCCGGATTCAGGGAAGCAGCTGGTGCACTACACAGCGCAGCCGCTGTTCCTGCTGGACCCCGGCTCC GTGGACACCGGGAGCAACGACCTGCCGGTGCTGTTTGAGCTGGGAGAGGGCTCCTACTTCTCCGAAGGGG ACGGCTTCGCCGAGGACCCCACCATCTCCCTGCTGACAGGCTCGGAGCCTCCCAAAGCCAAGGACCCCAC TGTCTCCTAGAGGCCCCGGAGGAGCTGGGCCAGCCGCCCACCCCCACCCCCAGTGCAGGGCTGGTCTTGG GGAGGCAGGGCAGCCTCGCGGTCTTGGGCACTGGTGGGTCGGCCGCCATAGCCCCAGTAGGACAAACGGG CTCGGGTCTGGGCAGCACCTCTGGTCAGGAGGGTCACCCTGGCCTGCCAGTCTGCCTTCCCCCAACCCCG TGTCCTGTGGTTTGGTTGGGGCTTCACAGCCACACCTGGACTGACCCTGCAGGTTGTTCATAGTCAGAAT TGTATTTTGGATTTTTACACAACTGTCCCGTTCCCCGCTCCACAGAGATACACAGATATATACACACAGT GGATGGACGGACAAGACAGGCAGAGATCTATAAACAGACAGGCTCTATGCTAAAAAAAAAAAAAAA Note: credit was given as long as the top two lines were present >gi|37574696|ref|NT_037704.4|Hs8_37708 Homo sapiens chromosome 8 genomic contig, reference assembly GAATTCTTTAAAAGTTCTGGCCAGGCATGGTGGCACACACCTGTAATCCCAGCACTTTGGGAGGCCAAGG Note: Only top two lines displayed to save space 3 pts. 2. a) This NCBI database contains information on human genes and diseases, as well as references and links to sequences and other genetics resources. Anyone can search the database for such information, although it is primarily for physicians, genetics students, and researchers. The page is not clear on exactly what disease information is contained. 1 pt. b) 117 1 pt. c) 32 1 pt. d) 8 1 pt. e) DYSTROPHIN; DMD MUSCULAR DYSTROPHY, DUCHENNE TYPE; DMD Note: The other result is for Dystrophin, the protein involved in DMD. There was no deduction for including this in your answer.