Team I Functional Annotation Group
Team 1 Functional Annotation
Team members: Kenji Gerhardt, Maria Ahmad, Manasa Vegesna, Shuheng Gan, and Hyeonjeong Cheon
Introduction
Background
Functional annotation is the process of associating predicted genes with their functional role in a cell. This includes the type of gene (translated/untranslated), their location within the cell, and their chemical and biological roles. These can be derived both by comparison to similar, already annotated genes with known (or anticipated) functions, or through ab initio annotation that relies on existing models, but which does not rely on databases of other annotated genes.
Objective
Our goal in this step is to functionally annotate the genes supplied to us by the gene prediction group.
Data
The genomes supplied to us were identified during assembly as E. coli. E. coli is the most highly studied microorganism: at present, NCBI contains 1072 complete E. coli genomes in its genome database, along with thousands of additional chromosomes, contigs, and scaffolds. This depth of study extends to its genes, where multiple pathogenic strains are identified and characterized well.
Pipeline
Pipeline image will be inserted
Clustering
Methods
Ab-initio Approach
Ab-Initio Tools predict and annotate different regions of the prokaryotic genome using 1) sequence composition, 2) likelihoods within the gene models, 3) gene content, and 4) ignal Detection. Ab-Initio Approach can be used for finding new genes, and no external data or evidence is needed for the prediction. However, it is limited by the presence of False Positives in the predicted data as well as over-prediction of small genes.
Homology-based Tools
Homology between genes means they share ancestry. Homologous genes that have recently diverged usually share function. We are looking to transfer annotation on known genes to our predicted genes by finding homology genes. Gene databases are collections of annotated genes. When we search a gene against a database, the search is looking for homology between our gene sequences and those in the database to determine what our genes’ function will be.
Prokka
Command:
prokka <contig.fa> --outdir <output directory> --prefix <file prefixes> --kingdom Bacteria --locustag --norrna --notrna