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Functional manual annotation including GO

Functional manual annotation including GO. Exercises for hands-on session. Type in “cell surface” and explore the results. Exercise 1: AmiGO search:. Exercise 1: AmiGO search , continued. What is the GO term accession for “cell surface? What is the definition of the “cell surface” term?

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Functional manual annotation including GO

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  1. Functional manual annotationincluding GO Exercises for hands-on session

  2. Type in “cell surface” and explore the results Exercise 1: AmiGO search:

  3. Exercise 1: AmiGO search , continued • What is the GO term accession for “cell surface? • What is the definition of the “cell surface” term? • Name one gene product that has the GO term “cell surface” annotated to it.

  4. Answers to Exercise 1: Amigo The cell surface GO ID is GO:0009986. The definition of the term is: The external part of the cell wall and/or plasma membrane. There are many gene products annotated with this term. Here are a few:

  5. Exercise 2: Functional Annotation Analyze and annotate the unknown T. brucei protein sequence T_brucei_unknown.fasta, which is on the flash drive in the functional_and_go directory. >unknown_T. brucei protein_sequence MLRRLGVRHFRRTPLLFVGGDGSIFERYTEIDNSNERRINALKGCGMFEDEWIATEKVHGANFGIYSIEGEKMIRYAKRSGIMPPNEHFFGYHILIPELQRYITSIREMLCEKQKKKLHVVLINGELFGGKYDHPSVPKTRKTVMVAGKPRTISAVQTDSFPQYSPDLHFYAFDIKYKETEDGDYTTLVYDEAIELFQRVPGLLYARAVIRGPMSKVAAFDVERFVTTIPPLVGMGNYPLTGNWAEGLVVKHSRLGMAGFDPKGPTVLKFKCTAFQEISTDRAQGPRVDEMRNVRRDSINRAGVQLPDLESIVQDPIQLEASKLLLNHVCENRLKNVLSKIGTEPFEKEEMTPDQLATLLAKDVLKDFLKDTEPSIVNIPVLIRKDLTRYVIFESRRLVCSQWKDILKRQSPDFSE*

  6. Analyze and annotate the sequence • Blast your sequence at NCBI, and interpret the results. • Use the Pfam site to search for Pfam and TIGRfamdomains. Use the Superfamily site to search for SCOP domains. Examine the output. • Search for families and motifs (Interpro, Prosite, SignalP, TargetP, TmHMM) and examine the output. • Summarize the results in an annotation. • Search for GO terms. Annotate all possible GO terms.

  7. Functional annotation of unknown T_brucei protein Summarize sequence homology: Domain(s): Motif(s): Name, or functional assignment: GO assignment(s): The annotations are in the Manual Functional Annotation and GO printouts, with the exception of additional GO term annotations.

  8. Additional possible GO term For RNA editing ligase: Cellular component: mitochondrion GO:0005739 (ISS with CBS:TargetP)

  9. Exercise 3: Functional Annotation Analyze and annotate the unknown Aedes aegypti protein sequence A_Aegypti_unknown.fasta, which is in your directory on the flash drive. >unknown_Aedes_aegypti_protein_85aa MASREAVRRAVQNVRPILSVDREEARKRVLNLYKAWYRQIPYIVMDYDIPKSVEQCREKLREEFLKHKNVTDIRVIDMLVIKGML

  10. Analyze and annotate the sequence • Blast your sequence at NCBI, and interpret the results. • Use the Pfam site to search for Pfam and TIGRFAMs domains. Examine the output. • Search for families and motifs (Interpro, Superfamily, Prosite, SignalP, TargetP, TmHMM) and examine the output. • Summarize the results in an annotation. • Search for GO terms. Annotate all possible GO terms.

  11. Annotation for Unknown Aedes aegypti protein sequence Summarize sequence homology: Domain(s) and Families: Motif(s): Name, or functional assignment: GO assignment(s): The annotations are in the Manual Functional Annotation printout, with the exception of GO term annotations.

  12. GO terms Predicted cellular component: mitochondrion GO:0005739 (ISS with CBS:TargetP) Predicted cellular component: Integral to membrane GO:0016021 (ISS with CBS:TMHMM) Predicted molecular function: NADH dehydrogenase (ubiquinone) activity GO:0008137 (ISS with UniProt:P56556 ) –deduced through sequence similarity (p-value 3.7e-16) using AmiGO BLAST function.

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