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== Sequence searches == [[Task 2 lab journal (MSUD)#Sequence searches|Lab journal]] === Results === The query sequences for the 4 subunits of BCKDC locate at <nowiki>/mnt/home/student/weish/master-practical-2013/task01/</nowiki>. Results for sequence search locate in the directory <nowiki>/mnt/home/student/weish/master-practical-2013/task02/01-seq-search/results</nowiki>. For BLAST and PSI-BLAST, statistics (such as E-value, probability and identity) are stored in <nowiki>*.tsv</nowiki> files. Detailed results are shown in xml files. For HHBlits, the <nowiki>*.hhr</nowiki> files contain information about statistics and hits. ==== BCKDHB ==== <gallery widths=500px heights=411px caption="E-value and identity distribution for different sequence search methods"> File:E-value-distribution BCKDHB.png|E-value distribution of sequence search methods. (Query sequence is RefSeq of BCKDHB) File:Identity distribution BCKDHB.png|Indentity distribution of sequence search methods. (Query sequence is RefSeq of BCKDHB) </gallery> <gallery widths=500px heights=400px perrow=2 caption="Intersection of hits between different sequence search methods"> File:Intersection to blast BCKDHB.png|Relative intersection of hits between BLAST and other sequence search methods. File:Intersection to psiblast(iter. 2, e-val. 0.002) BCKDHB.png|Relative intersection between PSI-BLAST(iter. 2, E-value 0.002) and other sequence search methods. File:Intersection to psiblast(iter. 2, e-val. 10e-10) BCKDHB.png|Relative intersection between PSI-BLAST(iter. 2, E-value 10e-10) and other sequence search methods. File:Intersection to psiblast(iter. 10, e-val. 0.002) BCKDHB.png|Relative intersection between PSI-BLAST(iter. 10, E-value 0.002) and other sequence search methods. File:Intersection to psiblast(iter. 10, e-val. 10e-10) BCKDHB.png|Relative intersection between PSI-BLAST(iter. 10, E-value 10e-10) and other sequence search methods. File:Intersection to hhblits BCKDHB.png|Relative intersection between HHBlits and other sequence search methods. </gallery> <gallery widths=500px heights=400px perrow=2 caption="Distribution of SCOP folds"> File:SCOP histogram blast BCKDHB.png|Distribution of SCOP fold in BLAST hits File:SCOP histogram psiblast(iter. 10, e-val. 10e-10) BCKDHB.png|Distribution of SCOP fold in hits of PSI-BLAST(iter. 10, E-value 10e-10) </gallery> <gallery widths=335px heights=267px perrow=3 caption="Top-5 common GO terms in hits with GO annotation"> File:GO histogram blast BCKDHB.png|Top-5 common GO terms in BLAST hits File:GO histogram psiblast(iter. 2, e-val. 0.002) BCKDHB.png|Top-5 common GO terms in hits of PSI-BLAST(iter. 2, E-value 0.002) File:GO histogram psiblast(iter. 10, e-val. 10e-10) BCKDHB.png|Top-5 common GO terms in hits of PSI-BLAST(iter. 10, E-value 10e-10) </gallery> ==== DBT ==== <gallery widths=500px heights=411px caption="E-value and identity distribution for different sequence search methods"> File:E-value-distribution DBT.png|E-value distribution of sequence search methods. (Query sequence is RefSeq of DBT) File:Identity distribution DBT.png|Indentity distribution of sequence search methods. (Query sequence is RefSeq of DBT) </gallery> <gallery widths=500px heights=400px perrow=2 caption="Intersection of hits between different sequence search methods"> File:Intersection to blast DBT.pdf.png|Relative intersection of hits between BLAST and other sequence search methods. File:Intersection to psiblast(iter. 2, e-val. 0.002) DBT.pdf.png|Relative intersection between PSI-BLAST(iter. 2, E-value 0.002) and other sequence search methods. File:Intersection to psiblast(iter. 2, e-val. 10e-10) DBT.pdf.png|Relative intersection between PSI-BLAST(iter. 2, E-value 10e-10) and other sequence search methods. File:Intersection to psiblast(iter. 10, e-val. 0.002) DBT.pdf.png|Relative intersection between PSI-BLAST(iter. 10, E-value 0.002) and other sequence search methods. File:Intersection to psiblast(iter. 10, e-val. 10e-10) DBT.pdf.png|Relative intersection between PSI-BLAST(iter. 10, E-value 10e-10) and other sequence search methods. File:Intersection to hhblits DBT.pdf.png|Relative intersection between HHBlits and other sequence search methods. </gallery> <gallery widths=500px heights=400px perrow=2 caption="Distribution of SCOP folds"> File:SCOP histogram psiblast(iter. 10, e-val. 0.002) DBT.png|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. </gallery> <gallery widths=335px heights=267px perrow=3 caption="Top-5 common GO terms in hits with GO annotation"> File:GO histogram blast DBT.png|Top-5 common GO terms in BLAST hits File:GO histogram psiblast(iter. 2, e-val. 0.002) DBT.png|Top-5 common GO terms in hits of PSI-BLAST(iter. 2, E-value 0.002) File:GO histogram psiblast(iter. 10, e-val. 10e-10) DBT.png|Top-5 common GO terms in hits of PSI-BLAST(iter. 10, E-value 10e-10) </gallery> ==== DLD ==== <gallery widths=500px heights=411px caption="E-value and identity distribution for different sequence search methods"> File:E-value-distribution DLD.png|E-value distribution of sequence search methods. (Query sequence is RefSeq of DLD) File:Identity distribution DLD.png|Indentity distribution of sequence search methods. (Query sequence is RefSeq of DLD) </gallery> <gallery widths=500px heights=400px perrow=2 caption="Intersection of hits between different sequence search methods"> File:Intersection to blast DLD.pdf.png|Relative intersection of hits between BLAST and other sequence search methods. File:Intersection to psiblast(iter. 2, e-val. 0.002) DLD.pdf.png|Relative intersection between PSI-BLAST(iter. 2, E-value 0.002) and other sequence search methods. File:Intersection to psiblast(iter. 2, e-val. 10e-10) DLD.pdf.png|Relative intersection between PSI-BLAST(iter. 2, E-value 10e-10) and other sequence search methods. File:Intersection to psiblast(iter. 10, e-val. 0.002) DLD.pdf.png|Relative intersection between PSI-BLAST(iter. 10, E-value 0.002) and other sequence search methods. File:Intersection to psiblast(iter. 10, e-val. 10e-10) DLD.pdf.png|Relative intersection between PSI-BLAST(iter. 10, E-value 10e-10) and other sequence search methods. File:Intersection to hhblits DLD.pdf.png|Relative intersection between HHBlits and other sequence search methods. </gallery> <gallery widths=500px heights=400px perrow=2 caption="Distribution of SCOP folds"> File:SCOP histogram blast DLD.png|Distribution of SCOP fold in BLAST hits File:SCOP histogram psiblast(iter. 10, e-val. 10e-10) DLD.png|Distribution of SCOP fold in hits of PSI-BLAST(iter. 10, E-value 10e-10) </gallery> <gallery widths=335px heights=267px perrow=3 caption="Top-5 common GO terms in hits with GO annotation"> File:GO histogram blast DLD.png|Top-5 common GO terms in BLAST hits File:GO histogram psiblast(iter. 2, e-val. 0.002) DLD.png|Top-5 common GO terms in hits of PSI-BLAST(iter. 2, E-value 0.002) 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) </gallery> === Discussion === == Multiple sequence alignment == === Results === === Discussion ===

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