Task 2 (MUSD) Additional Results

Sequence searches

Lab journal

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
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  E-value distribution of sequence search methods. (Query sequence is RefSeq of BCKDHB)

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  Indentity distribution of sequence search methods. (Query sequence is RefSeq of BCKDHB)

• Intersection of hits between different sequence search methods
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  Relative intersection of hits between BLAST and other sequence search methods.

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  Relative intersection between PSI-BLAST(iter. 2, E-value 0.002) and other sequence search methods.

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  Relative intersection between PSI-BLAST(iter. 2, E-value 10e-10) and other sequence search methods.

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  Relative intersection between PSI-BLAST(iter. 10, E-value 0.002) and other sequence search methods.

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  Relative intersection between PSI-BLAST(iter. 10, E-value 10e-10) and other sequence search methods.

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  Relative intersection between HHBlits and other sequence search methods.

• Distribution of SCOP folds
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  Distribution of SCOP fold in BLAST hits

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  Distribution of SCOP fold in hits of PSI-BLAST(iter. 10, E-value 10e-10)

• Top-5 common GO terms in hits with GO annotation
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  Top-5 common GO terms in BLAST hits

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  Top-5 common GO terms in hits of PSI-BLAST(iter. 2, E-value 0.002)

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  Top-5 common GO terms in hits of PSI-BLAST(iter. 10, E-value 10e-10)

DBT

• E-value and identity distribution for different sequence search methods
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  E-value distribution of sequence search methods. (Query sequence is RefSeq of DBT)

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  Indentity distribution of sequence search methods. (Query sequence is RefSeq of DBT)

• Intersection of hits between different sequence search methods
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  Relative intersection of hits between BLAST and other sequence search methods.

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  Relative intersection between PSI-BLAST(iter. 2, E-value 0.002) and other sequence search methods.

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  Relative intersection between PSI-BLAST(iter. 2, E-value 10e-10) and other sequence search methods.

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  Relative intersection between PSI-BLAST(iter. 10, E-value 0.002) and other sequence search methods.

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  Relative intersection between PSI-BLAST(iter. 10, E-value 10e-10) and other sequence search methods.

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  Relative intersection between HHBlits and other sequence search methods.

• Distribution of SCOP folds
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  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.

• Top-5 common GO terms in hits with GO annotation
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  Top-5 common GO terms in BLAST hits

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  Top-5 common GO terms in hits of PSI-BLAST(iter. 2, E-value 0.002)

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  Top-5 common GO terms in hits of PSI-BLAST(iter. 10, E-value 10e-10)

DLD

• E-value and identity distribution for different sequence search methods
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  E-value distribution of sequence search methods. (Query sequence is RefSeq of DLD)

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  Indentity distribution of sequence search methods. (Query sequence is RefSeq of DLD)

• Intersection of hits between different sequence search methods
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  Relative intersection of hits between BLAST and other sequence search methods.

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  Relative intersection between PSI-BLAST(iter. 2, E-value 0.002) and other sequence search methods.

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  Relative intersection between PSI-BLAST(iter. 2, E-value 10e-10) and other sequence search methods.

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  Relative intersection between PSI-BLAST(iter. 10, E-value 0.002) and other sequence search methods.

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  Relative intersection between PSI-BLAST(iter. 10, E-value 10e-10) and other sequence search methods.

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  Relative intersection between HHBlits and other sequence search methods.

• 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)

• Top-5 common GO terms in hits with GO annotation
• 

  Top-5 common GO terms in BLAST hits

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  Top-5 common GO terms in hits of PSI-BLAST(iter. 2, E-value 0.002)

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  Top-5 common GO terms in hits of PSI-BLAST(iter. 10, E-value 10e-10)

Multiple sequence alignment

Lab journal