A User's Guide to the Human Genome II

Spreading the word

• Alan Packer

Power to the people

• Andreas D. Baxevanis
• Francis S. Collins

Genomic empowerment: the importance of public databases

• Harold Varmus

A user's guide to the human genome

• Tyra G. Wolfsberg
• Kris A. Wetterstrand
• Andreas D. Baxevanis

Introduction: putting it together

Question 1 How does one find a gene of interest and determine that gene's structure? Once the gene has been located on the map, how does one easily examine other genes in that same region?

Question 2 How can sequence-tagged sites within a DNA sequence be identified?

Question 3 During a positional cloning project aimed at finding a human disease gene, linkage data have been obtained suggesting that the gene of interest lies between two sequence-tagged site markers. How can all the known and predicted candidate genes in this interval be identified? What BAC clones cover that particular region?

Question 4 A user wishes to find all the single nucleotide polymorphisms that lie between two sequence-tagged sites. Do any of these single nucleotide polymorphisms fall within the coding region of a gene? Where can any additional information about the function of these genes be found?

Question 5 Given a fragment of mRNA sequence, how would one find where that piece of DNA mapped in the human genome? Once its position has been determined, how would one find alternatively-spliced transcripts?

Question 6 How would one retrieve the sequence of a gene, along with all annotated exons and introns, as well as a certain number of flanking bases for use in primer design?

Question 7 How would an investigator easily find compiled information describing the structure of a gene of interest? Is it possible to obtain the sequence of any putative promoter regions?

Question 8 How can one find all the members of a human gene family?

Question 9 Are there ways to customize displays and designate preferences? Can tracks or features be added to displays by users on the basis of their own research?

Question 10 For a given protein, how can one determine whether it contains any functional domains of interest? What other proteins contain the same functional domains as this protein? How can one determine whether there is a similarity to other proteins, not only at the sequence level, but also at the structural level?

Question 11 An investigator has identified and cloned a human gene, but no corresponding mouse ortholog has yet been identified. How can a mouse genomic sequence with similarity to the human gene sequence be retrieved?

Question 12 How does a user find characterized mouse mutants corresponding to human genes?

Question 13 A user has identified an interesting phenotype in a mouse model and has been able to narrow down the critical region for the responsible gene to approximately 0.5 cM. How does one find the mouse genes in this region?

Commentary: keeping biology in mind

Acknowledgments

Web resources: Internet resources featured in this guide