Functional manual annotation including GO

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Presentation transcript:

Functional manual annotation including GO Exercises for hands-on session

Exercise 1: AmiGO search: 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? Name one gene product that has the GO term “cell surface” annotated to it.

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:

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*

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.

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.

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

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

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.

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.

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.