About Synteny Analysis
A one-page summary of the logic process used to determine if genes in a fosmid are syntenic with respect to D. melanogaster
A one-page summary of the logic process used to determine if genes in a fosmid are syntenic with respect to D. melanogaster
This document describes a protocol that GEP faculty can use to quickly identify potential errors in student gene annotations.
Three sample chimp chunk projects with student reports.
Following the step-by-step tutorial “Chimp BAC Analysis: Genes and Pseudogene”, students should be ready to annotate a chunk of chimpanzee DNA themselves, presenting evidence to support their claim of a gene or pseudogene. An example student report from the Bio 4342 course at WU is available here.
Brief guidelines with advice on annotating chimpanzee DNA, including what to put in the final report.
A step-by-step tutorial that takes the student through a gene identification problem in a chimpanzee BAC sequence using predictions from a gene prediction program (Genscan), the UCSC Browser and BLAST.
This exercise allows students to learn how to use mRNA and Expressed Sequence Tags (ESTs) evidence to assist their annotation efforts. An answer key is available for instructors.
This document describes the naming conventions used by NCBI. Students can use these naming conventions to quickly evaluate the type and the reliability of the sequences in the NCBI database.
This document provides a list of web-based annotation tools (and their web addresses) available to students.