Does your institution have a plan for BLAST?

Do you or your colleagues use NCBI’s BLAST algorithm to find and analyze biological sequences?

SRS Blast Results View

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
  • secure
  • 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

SRS 8.3.0.6 Update

A new update release for SRS has been made available – it includes a number of usability improvements to the web interface, additional tools to facilitate administration, as well as a range of performance and stability enhancements. The range of supported databanks has been growing steadily; recently support has been added for integration of the iRefIndex, MINT, BioGRID and DIP databanks on protein interaction data. More tools are now supported as well including GLSearch, GGSearc, FastF, FastS and FastM tools (part of the FASTA package) and Clustal Omega. Support for the latest version of the Hmmer package has been updated as well.

You can read the full release notes as well as download the software itself in the SRS 8.3 Downloads area.

BioWisdom SRS Adds Support for Chemistry Integration

BioWisdom is proud to announce the recent addition of support for chemistry searches and integration into the standard edition of our data search and retrieval platform, BioWisdom SRS.

SRS Chemistry SearchThis latest addition allows users unprecedented levels of integration of chemistry data with the wide range of public and proprietary datasets available within SRS. Starting from a structure of interest or a SMILES string, users can perform advanced searches into chemistry databases to identify related or structurally similar compounds.
Read more about BioWisdom SRS Adds Support for Chemistry Integration »

SRS 8.3.0.4 Patch Update

We have just released a new patch update for SRS 8.3. This latest update adds a number of new features, as well as general improvements in the usability and stability of SRS. There are about 20 new types of exports (including some new XML formats) available for various databanks in SRS and improved handling of binary data such as images or chemical structure files. There are a number of improvements in the layout and functionality of the web interface using the latest browsers, as well as improved compatibility with the latest platforms.

You can read the full release notes as well as download the software itself in the SRS 8.3 Downloads area.

The latest additions to the databases supported by SRS also include ChEMBL (a database of bioactive small molecules and their activities in biological systems), the KEGG Disease database – (part of the of the KEGG databases suite, describes various diseases, usually with a genetic component), the MEROPS peptidase database, HMDB (a database of compounds in the human metabolism, and the enzymes involved in their metabolization) and DrugBank (a drugs and protein/gene targets database).

You can keep up to date with the latest additions and changes to SRS parsers using the SRS 8.3 parser updates news feed.