Biocomputing Unit
Biocomputing
Sequence Analysis Service
Gibson Group
EMBL
EMBL

Predocs02 Course

Basic Tools in Sequence Analysis Practical

by Toby Gibson,Chenna Ramu , Aidan Budd and Francesca Diella, October 8-9th, 2001

Answers to Questions


Step 2 BLAST2 searching with human SM-B protein

Questions and Answers

Step 2B BLAST 2 search with SM-B and a filter

Questions and Answers


Step 3 Bic_SW search with human SM-B protein

Questions and Answers

Step3B Bic-SW search with the SM Domain only

Questions and Answers


Step 4. Bic_profilesearch based on an alignment of SM proteins

Step 4B. BIC_Profilesearch with an SM domain profile prepared with the Gonnet Pam250 matrix

Questions and answers


Step 5. Comparing a sequence to a database of protein domains

Questions and answers


Step 6. Looking for targeting signals in proteins by comparing sequences to a set of protein motifs

Questions and answers


Part 1 Take Home Lessons

Hopefully the exercise of varying the query type has illustrated that the way a search is set up is very important. The queries here illustrate the effect of different sequence types. There are other parameters that often influence the search sensitivity. For example when a globular domain is longer, the Gonnet Pam250 matrix would be expected to outperform the default Blosum62 in the detection of divergent homologues, because it is less stringent and so gives longer optimally matching segments. (Over short matches it is noisier and could perform worse). In fact we used the Gonnet matrix to make the profiles: because of the extra information in the alignment, profiles usually perform better with Pam250 than Blosum62. Also, gap penalties are critical parameters in dynamic programming and should always be tested by trial and error. In other words, it pays to try several variations in the searches, not just accept the results of the first search.


Part 2. Making multiple sequence alignments and calculating a tree.

Step 2. Aligning the elongation factor sequences with Clustal X

Questions and answers


Step 3. Calculating a tree with Clustal X and displaying it with NJplot

Questions and answers