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This Fall Semester, the Health Sciences Library Bioinformatics@HSL series is offering a set of three BLAST workshops which, taken together, constitute a short course in BLAST sequence similarity searching. Regardless of your level of skill this integrated “3-pack” of BLAST workshops will enhance your skill and efficiency using BLAST from the basics, through the tips and tricks I’ve gleamed from NCBI directly and working with others, through power BLASTing with PSI-BLAST and PHI-BLAST: two types of iterative BLAST search algorithms that can find structural, functional and/or sequence motif relationships for your sequence that “traditional” BLAST cannot.
Read over the workshop descriptions below and decide which work for you . You can then register for the workshops here, or, more importantly contact me at drein@buffalo.edu to arrange for the workshop to come on-site, tailored to your specific needs for your research laboratory, seminar, course, or group of any kind.
Don’t want BLAST? Want EndNote or something else instead? The BLAST Short Course is part of the HSL workshops offered every semester. If you are interested in EndNote, tenure metrics and more, take the opportunity to look over our other offerings and register for these courses as well. You can read about all of the HSL’s workshops, and then register for them, on HSL’s workshop webpage.
WORKSHOP 1: BLAST
BLAST, the Basic Local Alignment Search Tool from the National Center for Biotechnology Information (NCBI) at NIH, has become the major bioinformatics search tool to locate similar sequences to DNA or protein sequences. Proper analysis of BLAST results simultaneously provides insights into gene/protein structure and functions for unknown sequences while aiding in defining future experiments. A combination handout/workbook will be given to workshop participants that will cover the workshop material.
Following this workshop you will be able to:
- Search with BLAST.
- Decipher and analyze search results, including E values.
- Understand BLAST algorithmic interface options.
- Know the strengths and limitations of BLAST.
- Know how to choose between:
- Basic BLAST options (blastp, blastn, tblastn, blastx, etc.).
- Genomic BLAST.
- Specialized BLAST options (microarray, immunoglobulin, high-throughput sequencing, etc.).
- Use BLAST to align and compare sequences of your choice.
- Run mutation BLAST with either protein or nucleotide sequences.
- Edit, limit, and re-format both BLAST searches and results.
- Link-out from BLAST results to other related NCBI information for a given sequence.
- Manage BLAST search results.
TIMES AND LOCATIONS:
September 22, 2009: NORTH Campus— Room 212, Teaching & Learning Center, Capen Hall.
September 21, 2009: SOUTH Campus—Media Instruction Room, Health Sciences Library.
WORKSHOP 2: BLAST TIPS AND TRICKS
This two-hour practical hands-on workshop will focus to adjusting those BLAST algorithmic parameters which act as filters for BLAST, along with other “advanced commands” that can be used to enhance BLAST results. The workshop will concentrate primarily to nucleotide and protein BLASTing, but will cover other specialized BLAST searches based upon participant interest and available time. The new NCBI multiple alignment tool, COBALT, will also be introduced. A combination handout/workbook will be given to workshop participants that will cover the workshop material.
Following this workshop you will be able to:
- Constrain BLAST searches to specific sequence segments of your query using a variety of different methods.
- Limit the initial BLAST search to specific organisms, tissues of expression, molecule types or databases.
- Restrict the BLAST results to specific organisms, tissues of expression, molecule types or databases to make your analysis easier.
- Use filtering options to lower the number of statistically significant but meaningless hits to query sequences.
- Batch BLAST.
TIMES AND LOCATIONS:
September 28, 2009: SOUTH Campus—Media Instruction Room, Health Sciences Library.
September 29, 2009: NORTH Campus— Room 212, Teaching & Learning Center, Capen Hall.
WORKSHOP 3: BEYOND BLAST: POWERING UP YOUR SEQUENCE SIMILARITY SEARCHES WITH NCBI PSI-BLAST AND PHI-BLAST
Position-Specific Iterative (PSI) BLAST is a protein sequence search method that generates a protein search profile in place of the original BLAST algorithm. More importantly, you the searcher, choose the sequences you need to build the search profile for subsequent iterations. Pattern Hit Initiated (PHI)-BLAST BLAST is similar, with the notable exception that you can specify a protein motif or repeating protein element to build your protein profile. Both PSI-BLAST and PHI-BLAST provide a means to detecting distant functional relationships between proteins that are beyond the capability of BLAST. They are also the method of choice if “traditional” BLAST is returning too few of hits or unannotated hits. The recently re-formatted NCBI PHI- and PSI-BLAST interface and algorithms now put these powerful tools into the hands of all BLAST users. Additionally, both PSI- and PHI-BLAST are integrated with any 3D structures returned within the hits, aligning sequences recovered from a search to the target sequence. This two-hour workshop will work through the underlying concept of scoring matrices upon which PHI- and PSI BLAST are built upon and provide practical hands-on experience in PHI- and PSI-BLASTing. A combination handout/workbook will be given to workshop participants that will cover the workshop material.
Following this workshop you will be:
- Understand scoring matrices and their use in BLAST, PSI-BLAST and PHI-BLAST
- Know when and how to run PHI-BLAST and PSI-BLAST
- Able to link-out from PHI-BLAST results to discover gene and protein structural information for your query.
October 5, 2009: NORTH Campus— Room 212, Teaching & Learning Center, Capen Hall.
October 6, 2009: SOUTH Campus—Media Instruction Room, Health Sciences Library.
