Difference between revisions of "Task 2 (MUSD) Additional Results"
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| + | == Sequence searches == |
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| + | [[Task 2 lab journal (MSUD)#Sequence searches|Lab journal]] |
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=== Results === |
=== Results === |
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The query sequences for the 4 subunits of BCKDC locate at <nowiki>/mnt/home/student/weish/master-practical-2013/task01/</nowiki>. |
The query sequences for the 4 subunits of BCKDC locate at <nowiki>/mnt/home/student/weish/master-practical-2013/task01/</nowiki>. |
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File:GO histogram psiblast(iter. 10, e-val. 10e-10) DLD.png|Top-5 common GO terms in hits of PSI-BLAST(iter. 10, E-value 10e-10) |
File:GO histogram psiblast(iter. 10, e-val. 10e-10) DLD.png|Top-5 common GO terms in hits of PSI-BLAST(iter. 10, E-value 10e-10) |
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</gallery> |
</gallery> |
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| + | === Discussion === |
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| + | == Multiple sequence alignment == |
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| + | === Results === |
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| + | === Discussion === |
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Revision as of 16:33, 9 August 2013
Contents
Sequence searches
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.
BCKDHB
- E-value and identity distribution for different sequence search methods
E-value distribution of sequence search methods. (Query sequence is RefSeq of BCKDHB)
Indentity distribution of sequence search methods. (Query sequence is RefSeq of BCKDHB)
- Intersection of hits between different sequence search methods
Relative intersection of hits between BLAST and other sequence search methods.
Relative intersection between PSI-BLAST(iter. 2, E-value 0.002) and other sequence search methods.
Relative intersection between PSI-BLAST(iter. 2, E-value 10e-10) and other sequence search methods.
Relative intersection between PSI-BLAST(iter. 10, E-value 0.002) and other sequence search methods.
Relative intersection between PSI-BLAST(iter. 10, E-value 10e-10) and other sequence search methods.
Relative intersection between HHBlits and other sequence search methods.
_BCKDHB.png)
_BCKDHB.png)
_BCKDHB.png)
_BCKDHB.png)
- Distribution of SCOP folds
Distribution of SCOP fold in BLAST hits
Distribution of SCOP fold in hits of PSI-BLAST(iter. 10, E-value 10e-10)
_BCKDHB.png)
- Top-5 common GO terms in hits with GO annotation
Top-5 common GO terms in BLAST hits
Top-5 common GO terms in hits of PSI-BLAST(iter. 2, E-value 0.002)
Top-5 common GO terms in hits of PSI-BLAST(iter. 10, E-value 10e-10)
_BCKDHB.png)
_BCKDHB.png)
DBT
- E-value and identity distribution for different sequence search methods
E-value distribution of sequence search methods. (Query sequence is RefSeq of DBT)
Indentity distribution of sequence search methods. (Query sequence is RefSeq of DBT)
- Intersection of hits between different sequence search methods
Relative intersection of hits between BLAST and other sequence search methods.
Relative intersection between PSI-BLAST(iter. 2, E-value 0.002) and other sequence search methods.
Relative intersection between PSI-BLAST(iter. 2, E-value 10e-10) and other sequence search methods.
Relative intersection between PSI-BLAST(iter. 10, E-value 0.002) and other sequence search methods.
Relative intersection between PSI-BLAST(iter. 10, E-value 10e-10) and other sequence search methods.
Relative intersection between HHBlits and other sequence search methods.
_DBT.pdf.png)
_DBT.pdf.png)
_DBT.pdf.png)
_DBT.pdf.png)
- Distribution of SCOP folds
Distribution of SCOP fold in hits of PSI-BLAST(iter. 10, E-value 0.002). This is the only test run which have PDB hits with SCOP classification.
_DBT.png)
- Top-5 common GO terms in hits with GO annotation
Top-5 common GO terms in BLAST hits
Top-5 common GO terms in hits of PSI-BLAST(iter. 2, E-value 0.002)
Top-5 common GO terms in hits of PSI-BLAST(iter. 10, E-value 10e-10)
_DBT.png)
_DBT.png)
DLD
- E-value and identity distribution for different sequence search methods
E-value distribution of sequence search methods. (Query sequence is RefSeq of DLD)
Indentity distribution of sequence search methods. (Query sequence is RefSeq of DLD)
- Intersection of hits between different sequence search methods
Relative intersection of hits between BLAST and other sequence search methods.
Relative intersection between PSI-BLAST(iter. 2, E-value 0.002) and other sequence search methods.
Relative intersection between PSI-BLAST(iter. 2, E-value 10e-10) and other sequence search methods.
Relative intersection between PSI-BLAST(iter. 10, E-value 0.002) and other sequence search methods.
Relative intersection between PSI-BLAST(iter. 10, E-value 10e-10) and other sequence search methods.
Relative intersection between HHBlits and other sequence search methods.
_DLD.pdf.png)
_DLD.pdf.png)
_DLD.pdf.png)
_DLD.pdf.png)
- Distribution of SCOP folds
Distribution of SCOP fold in BLAST hits
Distribution of SCOP fold in hits of PSI-BLAST(iter. 10, E-value 10e-10)
_DLD.png)
- Top-5 common GO terms in hits with GO annotation
Top-5 common GO terms in BLAST hits
Top-5 common GO terms in hits of PSI-BLAST(iter. 2, E-value 0.002)
Top-5 common GO terms in hits of PSI-BLAST(iter. 10, E-value 10e-10)
_DLD.png)
_DLD.png)
