NCBI bioinformatics mini-courses are either problem based, such as "Identification of Disease Genes" or NCBI resource based such as "BLAST Quick Start". The courses are 2.5 hours in length with first hour and half devoted to an overview that is followed by a one hour hands-on session. Contact Medha Bhagwat if you have any questions or comments about the mini-courses.

The course provides an introduction to aspects of bioinformatics such as accessing, analyzing, and interpreting biological data using NCBI databases and tools. An analysis of the animal photoreceptor family is used to illustrate practical bioinformatics approaches to the study of sequence similarity, phylogenetic analysis, gene expression, homology, polymorphisms, 3-D structure and function. This course will be useful for non-biologists as well as biologists.

- Developed by Medha Bhagwat

Course No. 2 "Making Sense of DNA and Protein Sequences"

In this mini-course, we will find a gene within a eukaryotic DNA sequence. We will then predict the function of the implied protein product by seeking sequence similarities to proteins of documented function using BLAST and other tools. Finally, we will find a 3D modeling template for this protein sequence using a Conserved Domain Database Search.

During the first hour, an instructor will walk you through an analysis of an uncharacterized Drosophila melanogaster genomic sequence from the GenBank record AE003584 found in Notebook 1. During the second hour of the class, you will perform the same analysis on the genomic sequence contained in Notebook 2.

This mini-course describes how to combine the output of multiple prediction programs to find genes, promoters and other transcription-factor binding sites in human DNA sequences. To illustrate the method, an instructional program called Greengene will be used to integrate the output of several gene-finding tools. Greengene also allows a coding sequence and accompanying protein translation to be assembled from the exons detected by these programs. Because the output of several programs is integrated, exon selection is more reliable.

This mini-course deals with the identification of a disease gene using NCBI's human genome assembly. The reference genome assembly, along with integrated maps, literature, and expression information comprises a powerful discovery system for exploring candidate human disease genes. We will start with EST sequences obtained from a patient, identify the gene(s) expressing them, download their sequences, determine the exon-intron structure and identify known SNPs in the ESTs, if any, that may contribute to the disease phenotype.

We will learn to determine what is known about a disease and the gene associated with it. We will then elucidate the biochemical and structural basis for the phenotype caused by the mutant protein.

A practical introduction to the BLAST family of sequence-similarity search programs. Exercises range from simple searches to creative uses of the BLAST programs to perform specialized searches.

NCBI's Entrez Gene provides gene-based information such as chromosome location, sequence, expression, structure, function, and homology data. Each record represents a single gene from an organism. Entrez Gene includes organisms for which there is a RefSeq genome record.

In this course, we will learn how to obtain information about a human gene such as its mRNA and genomic sequence, gene structure (exon-intron locations), function and phenotypes associated with mutations. We will also learn how to determine whether the SNPs in the coding region of a gene are known to alter the function of the protein product .

Entrez Gene is the successor to LocusLink. The mini-course will cover the use of Entrez Gene to obtain the same information as was found in LocusLink. The course will also cover the advantages of Entrez Gene such as efficient searching options and availability of gene-specific information for all completely sequenced genomes, including bacteria and viruses.

This course covers how to visualize and annotate 3D protein structures using NCBI's Cn3D, identify conserved domain(s) present in a protein, seach for other proteins containing similar domain(s), explore a 3D modeling template for the query protein and find distant sequence homologs that may not be identified by BLAST.

NCBI's MapViewer can be used to visualize an organism's genome. The organisms represented in the Map Viewer include human, mouse, rat, zebrafish, mosquito, nematode, fruit fly, yeast, arabidopsis and others.

In this course, we will use the human genome Map Viewer. Used to view the NCBI assembly of the complete human genome, Map Viewer is a valuable tool for the identification and localization of genes that contribute to human disease. In this course, we will see how to view different human genome maps and make best use of them. For example, the EST map can be used to identify undocumented exons or generate the alternative splice variants of genes. We will learn to locate a human gene, download its sequence along with its upstream sequence (to analyze promoter regions), obtain exon-intron coordinates, find a possible splice variant and identify whether the variations in the gene are associated with a disease.

GenBank is a repository of nucleotide sequences from about 160,000 organisms. This course begins with a survey of different types of entries. Using a typical GenBank entry as a model, students will learn to understand the features annotated on it. The course will also cover how to submit sequences to GenBank and include an overview of the processing of the entries. Finally, students will learn how to efficiently search GenBank and download sequences.

- Developed by Medha Bhagwat

Entrez is the integrated, text-based search and retrieval system used at NCBI for the major databases, including PubMed, Nucleotide and Protein Sequences, Expression, PubChem (biological activities of small molecules), Protein Structures, Complete Genomes, Taxonomy, and others. Entrez provides links to related records within the database and between other databases in Entrez. Click here for a more detailed view that illustrates the links existing among various Entrez Databases.

This course will provide tips on effective searching in Entrez databases and accessing the records in various formats.

In this mini-course, you will learn how to access the microbial genome sequences and annotations, how to navigate through and download the gene and protein datasets, and will be introduced to the available genomic and comparative genomic analysis tools. The course will address practical discovery questions such as 'Are there identifiable genes in microbial genomes that may be horizontally transferred?' and 'What are the differences between closely-related pathogenic and non-pathogenic bacteria?'

Revised February 28, 2008

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