7  Summary

In these workshops, you have learned about pairwise sequence alignment, BLAST searches, and some of the many features of BLAST and related services at NCBI.

By working through the pairwise sequence alignment exercises and BLAST search scenarios, you have been using the same research-level tools that biologists and bioinformaticians use in their day-to-day work.

Things you have learned

By working through this material, you should now

  • understand the difference between global and local pairwise alignments, and how to interpret their results
  • know how to use the EMBOSS Water and Needle tools to obtain optimal pairwise alignments
  • be able to explain the output from the Water and Needle tools
  • be able to identify an unknown organism and its relatives from a 16S sequence
  • understand the main output from a BLAST search at NCBI
  • know how to use NCBI BLAST search output to find and use additional information about matching sequences
  • know how to identify the putative function of a protein and the organism from which it is likely to originate
  • be able to identify and name conserved domains of a protein, using the BLAST output
  • be able to use BLAST to obtain preliminary identifications for a section of genome

and, if you worked through all the stretch activities, you should be able to

  • use the graphical summaries to interpret similarities between query sequences and the matches reported by BLAST
  • find and explain a BLAST result’s multiple sequence alignment
  • find and explain a BLAST result’s distance tree and taxonomy information
  • use the taxonomic information in an NCBI BLAST result to understand relationships between matching sequences
  • use BLAST output to obtain information about conserved protein domains, using the CDD database
  • modify your search parameters for the same query sequence, using taxon filters to exclude organisms from your search and identify biologically-useful information
  • explain how the choice of database affects the accuracy and comprehensiveness of your results
  • use BLAST results at NCBI to obtain domain and structural information relevant to your protein
  • use the NCBI BLAST service to help visualise structures of homologues to your protein
Important

If you haven’t already, please don’t forget to complete the formative assessments. There is one for each scenario, and one for the pairwise sequence alignment exercises on MyPlace.

7.1 That’s it!

Thank you for taking part in this workshop. We hope you enjoyed it!

Tell us about problems with the workshop, what you liked, or how you think it can be improved!

We would be very grateful to hear feedback by email or through the GitHub repository Issues page.