1 / 7

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.

acandace
Download Presentation

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

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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

More Related