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Preparing Students for Annotation Projects – A Stepwise Approach to Bioinformatics Literacy

Learn a stepwise approach to develop bioinformatics literacy in students, covering DNA structure, mutations, enzyme pathways, sequence homology, and more. Includes practical exercises and genomic analysis.

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Preparing Students for Annotation Projects – A Stepwise Approach to Bioinformatics Literacy

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  1. Preparing Students for Annotation Projects – A Stepwise Approach to Bioinformatics Literacy Craig Laufer and Ann Findley

  2. Identify clear content/skill acquisition objectives at the introductory level  assures a profitable upper-division experience • Basic conceptual tenets – DNA structure function/relationships, mutations, operon structure, enzyme pathways, sequence homology, tree construction/interpretation, etc. • Basic bioinformational tools – BLAST, CLUSTALW, recognizing gene content/syntax, etc. • Annotation – correcting start codons & identifying ribosome binding sites - have proteins been labeled correctly? - is gene part of a recognizable operon? - all student-made changes must be documented/justified.

  3. An introductory exercise: Students are assigned an enzyme, must locate the enzyme in related organismsand provide requested information • Given an enzyme EC designation – provide name of enzyme, identify reaction catalyzed by this reaction and using available genomic databases, locate enzyme in an organism(s) of interest, and complete enzyme profile worksheet. • EC 6.3.4.14 – biotin carboxylase in Campylobacter jejuni (81-176 vs. 260.94) • Using IMG – provide aa length, identify COG and family designations, indicate KEGG and IMG pathways • Using IMG – generate ortholog neighborhoods • Using Protein database – provide protein alignment for enzyme in different strains of organism of interest

  4. Protein alignment of biotin carboxylase (6.3.4.14) in C. jejuni 81-176 vs. 260.94 • >ejuni • MEIKSILIANRGEIALRALRTIKEMGKKAICVYSEADKDALYLKYADASICIGKARSSESYLNIPAIITA • AEIAEADAIFPGYGFLSENQNFVEICAKHNIKFIGPSVEAMNLMSDKSKAKQVMQRAGVPVIPGSDGALA • GAEAAKKLAKEIGYPVILKAAAGGGGRGMRVVENEKDLEKAYWSAESEAMTAFGDGTMYMEKYIQNPRHI • EVQVIGDSFGNVIHVGERDCSMQRRHQKLIEESPAIL-LDEKTRTRLHETAIKAAKAIGYEGAGTFEFLV • DK-NLDFYFIEMNTRLQVEHCVSEMVSGIDIIEQMIKVAEGYALPSQESIKLNGHSIECRITAEDSKTFL • PSPGKITKYIPPAGRNVRME-SHCYQDYSVPPYYDSMIGKLVVWAEDRNKAIAKMKVALDELLISGIKTT • KDFHLSMMENPDFINNNYDTNYLARH • >carboxylase_81-176 • ME--------------KGLKV------KIVCVES-IDSTHLFL-------C-------EQIRN------- • ---GKIDGNFAIY-----------------------ALEQTNGVGSRENSWQ-----------SSKGNLH • LSFCIK----------------------------EEDL----------------------------PKDL • PLASVSIYFAYLLKE-----LLQEKGSKIWLKWPNDLYLDDK-------------KAGGVISAKISNFII • GGMGLNLKFSPQNTAL----CDIEILLK-DLVSEFLQKVEKKIL--WKNI-FSKYMLEF----EKSRKF- • --------SVHHEGKVFSLENSFLYEDGSI------LLG---------DKRVYSLR--------------

  5. From a chromosome map for the organism of interest – provide interpretation (Parkhill et al., Nature, 2000)

  6. Identify hypervariable sequences in C. jejuni – speculate on putative functions & effect on pathogenicity

  7. Identify the largest paralogous gene families in C. jejuni – Compare gene families across C. jejuni isolates, speculate on evolutionary advantage/operative selection pressure

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