Bio::POD

Uses

Bio::POD is most useful for small groups of researchers that are performing any type of screening that involves primer pair (oligonucleotide) selection for PCR reactions including single stranded conformational polymorphism (SSCP) and sequencing reactions. The PAR algorithm increases the efficiency of these research projects, saving your time and money. Bio::POD is intended for use in a research project involving a small to medium dataset of candidate genes.

The Bio::POD application is gene-centric, meaning that all of the data gathering and management is based on known or predicted genes. However, the system is flexible enough that it can be used with any type of sequence from any source. This just means that all of the data aggregation and automation may not be available to researchers who are not dealing with known genes as a primary position for screening.

Features

Bio::POD has a long list of features including, but not limited to:

• Prioritization of Annotated Regions (PAR)
  A unique prioritization algorithm developed and used by one of our academic collaborators [2], PAR is an innovative and exciting algorithm that will allow researchers to increase the efficiency of their screening projects. PAR is able to prioritize regions of a gene for mutation or sequence variation screening. This technique, coupled with automated data management, allows Bio::POD to take your screening projects to the next level in efficiency!
• Advanced Data Caching
  Bio::POD employs intelligent data caching that allows you quick access to your data, even if it is from large, remote public data sources. Data caching allows you access to your data even if the remote site is unreachable or you are working offline.
• Automated Data Aggregation
  Simplify your screening projects by letting Bio::POD do some of the work for you. Simply tell the program what types of data you are interested in, and a public data source to get it from, and the program will gather, reformat (if necessary), and display the data to you graphically. It can cut hours of web browsing and cutting and pasting on multiple genome browsers into minutes. And the next time that you launch the application you will have all of your data at your fingertips, allowing you to concentrate on the real work, your research.
• Automated Data Management
  Bio::POD manages your data without all of the hassle of notebooks, 3 ring binders, and multiple printouts. Get to all of your data in one place, and never again worry about losing track of what has been and what hasn't been done with your screening project.
• Custom Annotation
  As the amount of publicly available data continues to grow and change, the quality and goals of different data sources are beginning to diverge. The decisions made by the curators of these data sources may not be decisions that you agree with. Bio::POD returns the control of these decisions to you! You can create your own modified version of publicly available annotation, or even create new annotation that is not publicly available yet.
• Multiple Data Source Integration
  Bio::POD allows you to utilize public data sources as fully as possible. You are able to load the versions of the genes that you are interested in from any of several different public sources, and you can easily switch between data sources as often as you would like.

Screenshots

A screenshot of Bio::POD with the VAX2 gene loaded from Ensembl. The top window displays exons only (with UTR included), and annotation associated with the coding portion of a gene such as functional domains. The middle window shows the entire gene including introns, upstream and downstream sequence, and annotation that is not coding-specific such as SNPs. The graphs provide a visual representation of the PAR algorithm which suggests where to start screening the gene for variations.

This screenshot is of the same gene, except the zoom feature has been used to zoom in closer and view the nucleotide and amino acid sequence of the gene. Also, notice that a primer pair has been designed and is displayed in the middle window. The primer pairs are generated using primer3 [1].

Subscription types

Bio::POD is available under two different licenses:

Academic Subscription

The academic license is available to research professionals that are working at a qualified educational facility. The license cost is considerably smaller, but a full year support contract is required to get the lower price. Bio::Neos, Inc. reserves the right to determine what educational facilities qualify for the price discount.

Professional Subscription

The professional version of Bio::POD is the full release version with free minor-release upgrades, available but not required support costs, and a reduced upgrade fee for upcoming major releases.

Referral Program

If you know of someone who may benefit from Bio::POD, then please consider helping us get in touch with each other. Our Referral Program section has more details.

1. This product includes software which uses Primer3_1.0.0 developed by the Whitehead Institute for Biomedical Research
2. Braun, T.A., Shankar, S.P., Davis, S.G., O'Leary, B.M., Scheetz, T.E., Clark, A.F., Sheffield, V.C., Casavant, T.L., Stone. E.M. "Prioritizing Regions of Candidate Genes for Efficient Mutation Screening." Article accepted for publication in Human Mutation © Copyright 2005 Wiley-Liss, Inc. A Wiley Company