Task 2 (MUSD) Additional Results
The query sequences for the 4 subunits of BCKDC locate at /mnt/home/student/weish/master-practical-2013/task01/.
Results for sequence search locate in the directory /mnt/home/student/weish/master-practical-2013/task02/01-seq-search/results. For BLAST and PSI-BLAST, statistics (such as E-value, probability and identity) are stored in *.tsv files. Detailed results are shown in xml files. For HHBlits, the *.hhr files contain information about statistics and hits.
- E-value distribution:
- Very few hits were found with very low E-values. These hits have very high statistical significance.
- Because different databases were used for BLAST/PSI-BLAST and HHBLits, hhblits has found hits with larger range of e-value. HHblits found more frequently hits with high E-value.
- For protein BCKDHB, PSI-BLAST tends to find out more hits with intermediate E-value (1e-106 to 1e-25).
- E-value distribution of PSI-BLAST shift to low E-value side with more iterations. If we have chosen more iterations for PSI-Blast the shift of result space might be even larger. This phenomenon may cause PSI-blast to find out more hits that are over fitted to the statistical model but less hits with high biological significance. So there is a trade off between iteration number and result quality.
- Identity distribution
- Results show that BLAST depends mostly on sequence identity because most hits shift towards higher sequence identity. Hits with low sequence identity but high biological similarity may be lose in this case.
- Intersection of hits
- HHBlits was not comparable to other methods due to different sequence database. We were not able to find out the sequence ID from the results for HHBlits, which is important for getting the intersection of results.
- PSI-BLAST with 2 iterations has a result set of larger intersection with the result set of BLAST.
- Two PSI-BLAST runs with 2 iterations and different E-value cutoffs have very similar set of hits.
- PSI-BLAST with 10 iterations has less intersection with BLAST. This might be explained by the shift of result space by using PSI-Blast with higher number of iterations.
- Two PSI-BLAST runs with 10 iterations and different E-value cutoffs share the fewest common hits. It is possibly due to the effect of choice of E-value cutoff.
- SCOP of hit sequences
- PDB sequence required -> no evaluation for HHBlits
- Both BLAST and PSI-BLAST find the right fold class for the query proteins.
- PSI-BLAST generally find more hits in the fold class that describes the query protein best (e.g. DLD protein, c.3 is FAD/NAD(P)-binding domain)
- PSI-BLAST also finds out hits in more fold classes which may describe domains of query protein.
- PSI-Blast seems to find out more hits with biological significance.
- Gene Ontology of hit proteins
- Top-5 GO terms in hits of PSI-BLAST with different iterations are more conserved. They also have similar ranking of frequency.
- PSI-BLAST finds out hits with more GO terms. It may be more sensitive to functional patterns in sequence. Another explanation could be, due to the shift effect of result space, more irrelevant hits might be included which come with more different GO terms.
Multiple sequence alignments
In the following sections the MSAs, visualised with Jalview, are shown.