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BLAST

Sequence Similarity Introduction

This lesson and exercise defines similarity in a non-biological and biological sense, quantifies the similarity between two sequences, explains how a substitution matrix is used to quantify similarity, calculates amino acid similarity scores using the BLOSUM 62 substitution matrix, explains how BLAST detects similarity between two sequences and how to use BLAST and interpret the alignments.

Parasitoid Wasps Project: Annotation Walkthrough

This exercise will walkthrough an example of annotating a wasp venom gene for the Parasitoid Wasps Project. It will discuss wasp versions of common GEP annotation tools—Genome Browser, Gene Record Finder, and Gene Model Checker—and provide background for the interpretation of data tracks that are unique to the Parasitoid Wasps Project.

Annotation of Transcription Start Sites in Drosophila

This walkthrough illustrates the GEP protocol for the comparative annotation of transcription start sites (TSS) in D. biarmipes. The walkthrough also includes a sample GEP TSS Report for the TSS annotation of onecut.

Searching for Transcription Start Sites in Drosophila

This PowerPoint presentation describes the recommended annotation strategy for identifying transcription start sites in Drosophila. The presentation provides an overview of the promoter architecture in D. melanogaster and describes the types of evidence that can be used to support the transcription start sites annotations.

Annotation of Other Genomic Features within the F Element Project

This presentation illustrates the unusual genomic features that GEP students have encountered as part of their annotation of Muller F Elements from Drosophila ananassae and D. bipectinata. The Muller F Elements in these two species have undergone substantial expansion compared to D. melanogaster. The presentation describes the basic strategy for identifying pseudogenes, retrogenes, partial gene duplications, pseudogene clusters, and nuclear mitochondrial DNA segments (NUMT) within these F Element annotation projects.

Annotation Strategy Guide

This document illustrates how the strategies outlined in the Annotation Instruction Sheet can be applied to more challenging annotation cases.

Annotation Instruction Sheet

This document is a more in depth description of the evidence based annotation technique used by the GEP. This document is designed to complement and extend the basic technique described in the Annotation for D. virilis PowerPoint.

Annotation for D. virilis

This is a PowerPoint presentation describing the recommended strategies for annotating a D. virilis fosmid. The homology-based annotation strategy should also be applicable to annotation of D. erecta and D. mojavensis projects.

Annotation of Drosophila

This PowerPoint presentation describes the recommended annotation strategy for Drosophila projects. The presentation provides an overview of the goals of the GEP annotation project, an introduction to NCBI BLAST, web databases, and the issue of reading frames and phase.