Question

Which of the following does not constitute an online resource for aligning sequence pairs?

• A. BLASTX
• B. BCM Search Launcher
• C. SIM
• D. BLASTN

Hint:

To remember:
- BLAST family tools are hosted online by NCBI and other databases for high-speed, web-based sequence alignment.
- BCM Search Launcher is a historical online web portal.
- SIM is a localized command-line program.

Answer 1

The Correct Option is C

Step 1: Understanding the Concept:
Bioinformatics resources are divided into online platforms (web portals and database search systems) and stand-alone software tools or algorithms used for sequence alignment.

Step 3: Detailed Explanation:
Let us evaluate each of the listed resources:
- BLASTN (D): An online database search tool provided by NCBI.
It compares a nucleotide query sequence against a nucleotide database to find homologous pairs.
- BLASTX (A): An online NCBI tool that translates a nucleotide query sequence in all six reading frames and compares it against a protein database.
- BCM Search Launcher (B): Developed by the Baylor College of Medicine, this is a web-based portal (online resource) that bundles multiple sequence alignment and database search tools into a single user interface.
- SIM (C): This is a stand-alone computer program developed by Xiaoqiu Huang and Webb Miller.
It uses a dynamic programming algorithm to find local alignments between two protein sequences.
While it is an alignment tool, SIM itself is a local computer utility rather than an online database or web portal resource.
Therefore, SIM does not constitute an online resource for aligning sequence pairs.

Step 4: Final Answer:
The option that is not an online database search or alignment resource is SIM, matching Option (C).