microgen - the laboratory for genomics and bioinformatics

Comput-bio-info-what? September 2005
What is bioinformatics? What is it useful for? What are some real world applications? Can I get a job in bioinformatics? Many students and faculty have questions like these concerning bioinformatics and this monthly bulletin is created with the intent to answer these questions and many more like them. My goal is to provide faculty and students every month with information about bioinformatics in an effort to capture their interest in this growing and exciting field. (download)

Introduction to Biological Databases October 2005
One major desire of scientists is to understand in detail the relationship between the genome and the metabolic processes of an organism. Couple this with the desire with the advancing efficiency of high-throughput technology, and you have a scenario that produces a plethora of biological data that needs to be managed, organized, characterized and interpreted to extract meaningful information. To meet this need, public biological databases have arisen as vital resources to the scientific community. Because of their rising importance to science, it is important to be awar of the different databases that are available. This bulletin will introduce you to different types of databases that exist and to examples of some of the most popular databases. (download)

Pairwise Sequence Alignments November 2005
One focus of many scientists today is to determine if two sequences are related by the sharing of similar functional domains or sequence motifs. Through analysis of DNA and protein sequences, it is possible to determine if two sequences are significantly similar at the sequence level, which suggests tht they are homologous. Determining that two sequences are related indicates that they could have a common function, similar 3-D structure and common functinoal domains, providing many potential uses in genomics, proteomics, pharmacogenomics and other fields. (download)

Introduction to NCBI Databases December 2005
This month's bulletin will briefl cover database searching on the National Center for Biotechnology Information (NCBI) website. NCBI is dedicated to developing "new information technologies to aid in the understanding of fundamental molecular and genetic processes that control health and disease" (www.ncbi.nlm.nih.gov/About/glance/ourmission.html). This website is one of the major resources for a large number of databases that contain different types of biological information, ranging from nucleic acid and amino acid sequence information to taxonomic information and three-dimensional structures of proteins and conserved domains. (download)

What is BLAST? January 2006
The fundamental way of learning about a protein or gene is to compare it to well-known proteins or genes. With the large number of sequence databases available, an investigator can search through millions of characterized (and uncharacterized) sequences for one or more sequences that are similar to a query sequence. He or she can search through a list of significant alignments from a sequence similarity search and explore the similarities and differences between the query sequence and the significantly matching sequences. The Basic Local Alignment Search Tool (BLAST) is the main sequences similarity search tool for just such a task. In this month's bulletin, I will introduce you to BLAST: how it can be used, what BLAST algorithms are available, how it works, how to interpret the results and where you can find it. (download)

Phylogenetic Analysis February 2006
The revolution in the acquisition of nucleotide sequence data, as has been outlined in earlier versions of this newsletter, has been especially supportive in revealing the evolutionary history of life on earth. Over time, the field of phylogenetics has become increasingly diverse, with its own terminology as well as methodological variants. The links following this article will provide information on its terminology and methodological background. This newsletter is intended only to introduce the bioinformatics tools that are available to practitioners in the field. Generally speaking, these tools are used to either elucidate the relationships of a group of organisms, or to trace evolutionary history of a specific set of characteristics. (download)

Signature Database "InterPro" March 2006
         If DNA is the blueprint of a cell, then the proteins are the materials that gives the cell its characteristics. Proteins serve any number of different roles, including structural, signaling, enzymatic and also transport. Knowing a proteins biological role is essential for understanding their important contribution to the overall biology of the organism.
         Once a new organism is sequences, scientist must analyze the raw sequence data to extract meaningful information from it. The very first task is to locate the potential open reading frames using gene finding tools such as Glimmer. Secondly, the annotator must identify and describe the function of the protein sequence encoded by the predicted open reading frame, which is a critical step following any sequencing project.
         One of the more popular methods for analyzing a novel protein sequence is to compare it to "protein signatures." A protein signature can be thought of as ... (download)

A Career in Bioinformatics April 2006
... Where a bioinformaticist can find work is a good place to begin when discussing possible career paths in this field. Popular places to find work are genome sequencing facilities that take on the challenge of completely sequencing entire genomes. In these laboratories bioinformaticists are needed not only to assemble millions of sequence fragments of a genome, for example, but also to analyze the resulting gene and protein sequences during annotation. The quality of the annotation is extremely important because this will bring biological meaning to the sequence data. Also the bioinformaticist must be able to create and maintain databases to organize the large amount of data being produced by the sequencing technicians. (download)