Difference between revisions of "Sequence Alignments Hemochromatosis"

From Bioinformatikpedia
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</figtable>
 
</figtable>
   
The first BLAST search against the Big80 database reached the hit limit of 250 sequences with an E-Value of e-30 for the worst hit. So we did it again with a new limit of 1500 reported hits. These hits were then filtered for unique IDs and a E-Value cutoff of 2e-3. After the filtering 1159 hits were left.
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The first BLAST search against the Big80 database reached the hit limit of 250 sequences with an e-Value of e-30 for the worst hit. So we did it again with a new limit of 1500 reported hits. These hits were then filtered for unique IDs and an e-Value cutoff of 2e-3. After the filtering 1159 hits were left.
   
The distributions for the E-Values and Identities of these hits are shown in <xr id="blastdist"/>. Most of the E-Values are between 1e-50 and 2e-3 (cutoff). Only few hits have a better E-Value. The Identities are piled between 20% and 40% with two peaks at around 27% and 34% respectively.
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The distributions for the e-Values and identities of these hits are shown in <xr id="blastdist"/>. Most of the e-Values are between 1e-50 and 2e-3 (cutoff). Only few hits have a better e-Value. The identities are piled between 20% and 40% with two peaks at around 27% and 34% respectively.
   
 
=== PSI-Blast ===
 
=== PSI-Blast ===

Revision as of 10:03, 7 May 2012

Henry Frankenstein: Look! It's moving. It's alive. It's alive... It's alive, it's moving, it's alive, it's alive, it's alive, it's alive, IT'S ALIVE!

Victor Moritz: Henry - In the name of God!

Henry Frankenstein: Oh, in the name of God! Now I know what it feels like to be God!

Task Description

Protocol

Sorry for the inconvenience (not beeing able to read something), we're rerunning some data...

Protocol

Reference Sequence

Sequence from Uniprot: Q30201

>sp|Q30201|HFE_HUMAN Hereditary hemochromatosis protein OS=Homo sapiens GN=HFE PE=1 SV=1
MGPRARPALLLLMLLQTAVLQGRLLRSHSLHYLFMGASEQDLGLSLFEALGYVDDQLFVF
YDHESRRVEPRTPWVSSRISSQMWLQLSQSLKGWDHMFTVDFWTIMENHNHSKESHTLQV
ILGCEMQEDNSTEGYWKYGYDGQDHLEFCPDTLDWRAAEPRAWPTKLEWERHKIRARQNR
AYLERDCPAQLQQLLELGRGVLDQQVPPLVKVTHHVTSSVTTLRCRALNYYPQNITMKWL
KDKQPMDAKEFEPKDVLPNGDGTYQGWITLAVPPGEEQRYTCQVEHPGLDQPLIVIWEPS
PSGTLVIGVISGIAVFVVILFIGILFIILRKRQGSRGAMGHYVLAERE

Sequence Searches

Blast

<figtable id="blastdist">

Hemo eval blast 80.png
Hemo ident blast 80.png
Table 1: E-Value and identity distributions of the Blast search within Big80.

</figtable>

The first BLAST search against the Big80 database reached the hit limit of 250 sequences with an e-Value of e-30 for the worst hit. So we did it again with a new limit of 1500 reported hits. These hits were then filtered for unique IDs and an e-Value cutoff of 2e-3. After the filtering 1159 hits were left.

The distributions for the e-Values and identities of these hits are shown in <xr id="blastdist"/>. Most of the e-Values are between 1e-50 and 2e-3 (cutoff). Only few hits have a better e-Value. The identities are piled between 20% and 40% with two peaks at around 27% and 34% respectively.

PSI-Blast

<figtable id="psiblastdist">

Hemo eval psi 80.png
Hemo ident psi 80.png
E-Value and identity distributions of the PSI-BLast search within Big80.

</figtable>

HHblits

<figtable id="hhblitsdist">

Hemo eval hhblits 80.png
Hemo ident hhblits 80.png
E-Value and identity distributions of the HHblits search within Uniprot20.

</figtable>

Comparison

<figtable id="psiblastoverlap">

Hemo Overlap PSI.png
Hemo Overlap PSI BIG.png
Hemo Overlap PSI BLAST.png
Nothing to see here....

</figtable>

<figtable id="alloverlap">

Hemo Overlap All 80.png
Hemo Overlap All BIG.png
Hemo Overlap PSI HHB BIG.png
Nothing to see here....

</figtable>

Multiple Sequence Alignments

Dataset

CLustalW

Muscle

T-Coffee