Difference between revisions of "Sequence and multiple alignments"

From Bioinformatikpedia
(→‎Sequence Alignments)
(→‎Multiple Alignments)
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=Multiple Alignments=
  
=Multiple Alignments=
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== Multiple Alignments ==
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Used Sequences
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{| border="1" style="text-align:center; border-spacing:0;"
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!SeqIdentifier
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!Seq Identity
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!source
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!Protein function
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|-
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!colspan="4"| 99-90% Sequence Identity
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|-
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|xxx||%|| xxx || xxx
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|-
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|xxx||%|| xxx || xxx
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|-
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|xxx||%|| xxx || xxx
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|-
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|xxx||%|| xxx || xxx
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|-
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|xxx||%|| xxx || xxx
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|-
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!colspan="4"| 89-60% Sequence Identity
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|-
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|xxx||| % || xxx || xxx
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|-
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|xxx||%|| xxx || xxx
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|-
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|xxx||%|| xxx || xxx
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|-
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|xxx||%|| xxx || xxx
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|-
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|xxx||%|| xxx || xxx
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|-
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!colspan="4"| 59-40% Sequence Identity
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|-
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|xxx||%|| xxx || xxx
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|-
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|xxx||%|| xxx || xxx
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|-
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|xxx||%|| xxx || xxx
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|-
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|xxx||%|| xxx || xxx
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|-
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|xxx||%|| xxx || xxx
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|-
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!colspan="4"| 39-20% Sequence Identity
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|-
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|xxx||%|| xxx || xxx
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|-
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|xxx||%|| xxx || xxx
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|-
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|xxx||%|| xxx || xxx
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|-
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|xxx||%|| xxx || xxx
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|-
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|xxx||%|| xxx || xxx
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|}
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The sequences with <20% and >99% sequence identitiy were ignored and 5 samples were randomly picked from the other ranges. So 20 sequences were available for the multiple alignments. Unfortunately no sequences in the range between 99-90% with known 3D-structure were found, so only sequences without known structure were used here.

Revision as of 18:23, 23 May 2011

Sequence Alignments

Blastaufruf: blast -p blastp -i 1a6z.fasta -d /data/nr/nr -o blastp_1a6z_on_NR.txt runtime 5:34
Fastaaufruf: ../../Desktop/fasta-36.3.4/bin/fasta36 -q 1a6z.fasta /data/nr/nr >fasta_1a5z_on_nr.txt runtime 10:44

psiblast: blastpgp -i 1a6z.fasta -d /data/nr/nr runtime 21:40
blastpgp -i 1a6z.fasta -d /data/nr/nr -j 6 -e 10E-6 > psiblast_on_NR_itera3_e-val_10E-6.txt runtime 23:49
blastpgp -i 1a6z.fasta -d /data/nr/nr -j 3 -e 10E-6 > psiblast_on_NR_itera6_e-val_10E-6.txt runtime 15:08
blastpgp -i 1a6z.fasta -d /data/nr/nr -j 3 > psiblast_on_NR_itera3.txt runtime 9:41
blastpgp -i 1a6z.fasta -d /data/nr/nr -j 6 > psiblast_on_NR_itera6.txt runtime 23:30

Overlap.png

Multiple Alignments

Multiple Alignments

Used Sequences

SeqIdentifier Seq Identity source Protein function
99-90% Sequence Identity
xxx % xxx xxx
xxx % xxx xxx
xxx % xxx xxx
xxx % xxx xxx
xxx % xxx xxx
89-60% Sequence Identity
xxx % xxx xxx
xxx % xxx xxx
xxx % xxx xxx
xxx % xxx xxx
xxx % xxx xxx
59-40% Sequence Identity
xxx % xxx xxx
xxx % xxx xxx
xxx % xxx xxx
xxx % xxx xxx
xxx % xxx xxx
39-20% Sequence Identity
xxx % xxx xxx
xxx % xxx xxx
xxx % xxx xxx
xxx % xxx xxx
xxx % xxx xxx


The sequences with <20% and >99% sequence identitiy were ignored and 5 samples were randomly picked from the other ranges. So 20 sequences were available for the multiple alignments. Unfortunately no sequences in the range between 99-90% with known 3D-structure were found, so only sequences without known structure were used here.

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