Difference between revisions of "Sequence Alignments Hemochromatosis"
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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 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. Only 6 of these were PDB-IDs. |
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. |
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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Revision as of 10:12, 7 May 2012
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Contents
Task Description
Protocol
Sorry for the inconvenience (not beeing able to read something), we're rerunning some data...
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">
| 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. Only 6 of these were PDB-IDs.
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">
| E-Value and identity distributions of the PSI-BLast search within Big80. |
</figtable>
HHblits
<figtable id="hhblitsdist">
| E-Value and identity distributions of the HHblits search within Uniprot20. |
</figtable>
Comparison
<figtable id="psiblastoverlap">
| Nothing to see here.... |
</figtable>
<figtable id="alloverlap">
| Nothing to see here.... |
</figtable>
