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MERLOT II


    

Peer Review


Blast

 

Ratings

Overall Rating:

4.83 stars
Content Quality: 5 stars
Effectiveness: 4.5 stars
Ease of Use: 4.5 stars
Reviewed: Mar 16, 2004 by Biology Editorial Board
Overview:

BLAST? (Basic Local Alignment Search Tool) is a set of similarity search programs designed to explore all of the available sequence databases regardless of whether the query is protein or DNA. It offers the ability to compare sequences to a wide range of databases or the entire collection. These are tools developed by the molecular biology for the molecular biology community and are under constant upgrading. In addition, there are extensive materials for learning to use this tool box.This is primarily designed as a research tool, but can be adapted to educational use with some training and instruction. These algorithms may be used to rapidly search databases containing biological sequence information (protein and nucleic acid) for highly similar sequences or for local regions of sequence similarity imbedded in somewhat dissimilar sequences. Properly interpreted, these alignments may provide clues as to the function of newly discovered sequences and to evolutionary relationships between sequences. The page also links to tutorial programs, troubleshooting pages and FAQs. At the time of this review, the site had last been updated on February 10, 2004 and was running BLAST version 2.2.8.

Learning Goals:

  • Reinforcing basic biological concepts including the central dogma, mutation and evolution
  • Introduction to bioinformatics as a discipline
  • Introduction to powerful and current research tools
  • Introduction to comparative genomics
  • Choose appropriate BLAST tools that addressed the question being asked.
  • Search the biological sequences databases, and limit the searches to specific organisms and other subsets of sequences.
  • Search for motifs.
  • Compare multiple sequences from an alignment.
  • Interpret the output of the BLAST tools.
Target Student Population:

The site is intended for the research community, but with the proper materials and guidance, this tool could be useful for students from high school on up.

Prerequisite Knowledge or Skills:

To make effective use of this site, students will require a solid grasp of the basic tenets of molecular biology and, especially, the central dogma. Basic computer skills are also required. Even with the tutorials, most students will require some guidance from knowledgeable instructors to get started as the number of specific programs available could be intimidating to the novice.

Type of Material:

Database, Web-based interactive tool and tutorial

Recommended Uses:

With some guidance from instructors the BLAST programs can be used to reinforce concepts taught in biology courses such as gene expression, identification of open reading frames, processing of RNA, the modular nature of proteins, mutation evolution and others. Depending on the sophistication of the students this tool kit could be used in many ways. Beginning with introductory biology students, the tool would best be used as part of a guided activity with copious instructor attention, but more advanced students should be able to progress to using this tool kit in independent study activities either in or out of class.

Technical Requirements:

html


Evaluation and Observation

Content Quality

Rating: 5 stars
Strengths:

  • Highest quality database of protein and DNA sequences.
  • Updated regularly.
  • Several programs available to analyze data in database.
  • Students are working with the most current tools and data sets available.
  • The NCBI BLAST site contains state-of-the-art programs used by researchers around the world to analyze biological sequence information.
  • The use of a ?gateway page? with links to tutorials, a glossary, and the programs themselves is particularly effective given the number of related algorithms available to the user.
  • Material is updated frequently and the tutorials for the most part are useful for users of varying skill levels.
Concerns:

  • While primarily used as a research tool, bioinformatics will soon come to be viewed as an essential component of an undergraduate education in the biological sciences. Perhaps the authors will soon consider development of a simplified module designed specifically for educational purposes at the undergraduate level.

Potential Effectiveness as a Teaching Tool

Rating: 4.5 stars
Strengths:

  • This is a perfect tool for inquiry based exercises, by varying the any of the parameters of the assignment each one will be different.
  • Students are working with real datasets.
  • The tools are richly documented and there are tutorials to guide users through specific analyses.
  • As students progress they will be using the same tools even through their professional lives
  • Easy to make assignments using this database.
  • Once students are familiar with the site it is easy to navigate.
  • Great for open-ended or inquiry-based learning.
  • BLAST and PSI-BLAST tutorials are great, but students may still need a lot of guidance.
  • The NCBI BLAST site is an essential component of modern molecular research and as such deserves to be a component of a well-rounded education in the biological sciences.
  • Exposing students to state-of-the-art bioinformatics tools allows students to see how knowledge gained in the classroom is applied in solving problems in the real world.
  • Aligning biological sequences reinforces concepts and allows students to see relationships between information learned in separate classes. Interpreting data in the form of alignment outputs strengthens problem-solving skills.
  • Perhaps most importantly students using this site are exposed to a rapidly evolving discipline in which much opportunity exists for the foreseeable future.
Concerns:

  • The learning curve can be steep with this program. The tools are not intuitive to a beginning user.
  • The tutorials are appropriate for professional users and graduate students, but will need significant interpretation for use by other students.
  • Understanding how the programs work is much more complicated than having students just use them.
  • The authors may wish to communicate with educators to develop specific exercises target at undergraduates with varying levels of preparation to reinforce key concepts taught in classes at any institution and to make these available to educators who are less familiar with these bioinformatics tools.

Ease of Use for Both Students and Faculty

Rating: 4.5 stars
Strengths:

  • The NCBI BLAST page is accessible to essentially all students with a computer and the site is quite easily navigated.
  • Instructions for the use of the various algorithms are detailed and the servers at NCBI are powerful and fast in response times given the magnitude of computationally intense operations performed.
  • Bugs are quickly identified and corrected.
  • This is a highly reliable and responsive site.
  • As this is a professional tool, it is worth it for the student to invest time in learning to use this tool.
  • There is parameter specific help built-in to the tools to help understand what the parameters control.
  • Searchable, fast and reliable.
  • Well organized and maintained.

Concerns:

  • The vocabulary used in the tutorials is likely unfamiliar to most students as entry-level users and this tends to heighten the students? sense of frustration when first using the site.
  • The interpretation of the output is complex and at times not well explained for novice users (for example, in the blast 2 sequences tutorial).
  • Perhaps the authors could develop a primer for the novice user and allow more detail to be given only when the basics are introduced and reinforced.
  • Can be intimidating for first time users.
  • Output can be confusing to interpret for students.
  • The tutorials are appropriate for professional users and graduate students, but will need significant interpretation for use by other students.
  • Tutorials for novice, beginning users that uses language more appropriate to their level would be helpful.

Other Issues and Comments:

An indispensible tool for molecular research and a great training tool for students.
This site is a top candidate for MERLOT users to create assignments...hint, hint.