Do you or your colleagues use NCBI’s BLAST algorithm to find and analyze biological sequences?
In a BeyeNetwork article, Dr. Richard Casey asserts what many of us have suspected for over a decade: BLAST is probably the most widely used bioinformatics program. Here’s a small list of tasks that are enabled by BLAST (see also http://www.ncbi.nlm.nih.gov/books/NBK21097/ ):
- inferring the function of newly sequenced genes
- exploring evolutionary relationships: I am trying to develop a drug targeting HMG-CoA reductase in humans. Is the rat homolog similar enough that I don’t need to use primates in my studies?
- exploring the known natural diversity of genes similar to your gene of interest
- keeping on top of intellectual property concerns: Has anyone submitted a patent for an enzyme that I want to commercialize?
Many scientists are exposed to NCBI’s BLAST web interface as part of their academic training. Due to this familiarity, they may be inclined to use the NCBI interface whenever they need to do a BLAST analysis. But how can you protect the intellectual value of your sensitive queries if they are being sent over the public internet? And naturally, if the scientists in your organization are using NCBI’s BLAST web interface, they will be limited to searching against the databases that NCBI provides. If your organization has gone to the trouble to sequence some genomes, you are going to need a local solution for BLASTing those genomes.
Over the years, there have been open source initiatives for locally-deployed web-based BLAST interfaces, but over the long-term, they are usually poorly maintained, with no single point of accountability for support. Many of these tools are free only for academic or non-profit institutions. Perhaps of greatest concern, these tools tend to be analytical dead-ends or offer just a single view of the results. In contrast, Instem Scientific SRS is a true data integration platform. Any BLAST analysis carried out in SRS is just the starting point for subsequent analyses, like a multiple sequence alignment. You can also link to pages for your BLAST hits in their original, rich format. Multiple canned or user-generated views help you make sense of large result sets, as do filtering and sorting options.
Organizations that recognize the limitations of NCBI’s public BLAST interface or open-source BLAST interface often initiate in-house development of a BLAST interface from scratch. In some organizations you will even find multiple efforts like this. Is maintaining a custom BLAST interface the best use of your highly-skilled and highly-compensated bioinformatics developers’ time? Shouldn’t they be focusing their efforts on innovative solutions within your business domain?
If you are using a home-brewed BLAST interface, do you have a plan for accommodating changes in the blast binaries? For example, have you made the recommended migration to blast+? How agile can you be in accommodating new command line parameters or new output formats? Subscribers to SRS maintenance receive parser updates several times throughout the year to accommodate these kinds of changes to bioinformatics applications and file formats.
For those of you who have an in-house BLAST interface, how do you keep up to date with your BLAST database sources? The optional SRS Prisma module downloads and formats the latest version of common sequence databases. Even seasoned bioinformaticians who prefer to work from the command line will benefit from the up-to-date, centralized BLAST databases delivered by Prisma.
Your organization needs a plan for a BLAST interface that is
- easy to use
- scales well for multiple users
- comes with a commitment for support
Instem Scientific’s SRS meets all of these requirements. Don’t let such an important tool become an afterthought in your institution – SRS has a decades-long track record of providing reliable BLASTing to institutions of all sizes