Difference between revisions of "Fabry:Sequence alignments (sequence searches and multiple alignments)/Journal"
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Please see [[Fabry:Sequence_alignments_(sequence_searches_and_multiple_alignments):Results | Task 2 Results]] for our results on this topic. |
Please see [[Fabry:Sequence_alignments_(sequence_searches_and_multiple_alignments):Results | Task 2 Results]] for our results on this topic. |
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| + | == Reference sequence == |
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| + | The reference sequence of [[Alpha-galactosidase|α-Galactosidase A]] that will be used in the following tasks was obtained from Swissprot [http://www.uniprot.org/uniprot/P06280 P06280]. |
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| + | >gi|4504009|ref|NP_000160.1| alpha-galactosidase A precursor [Homo sapiens] |
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| + | MQLRNPELHLGCALALRFLALVSWDIPGARALDNGLARTPTMGWLHWERFMCNLDCQEEPDSCISEKLFM |
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| + | EMAELMVSEGWKDAGYEYLCIDDCWMAPQRDSEGRLQADPQRFPHGIRQLANYVHSKGLKLGIYADVGNK |
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| + | TCAGFPGSFGYYDIDAQTFADWGVDLLKFDGCYCDSLENLADGYKHMSLALNRTGRSIVYSCEWPLYMWP |
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| + | FQKPNYTEIRQYCNHWRNFADIDDSWKSIKSILDWTSFNQERIVDVAGPGGWNDPDMLVIGNFGLSWNQQ |
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| + | VTQMALWAIMAAPLFMSNDLRHISPQAKALLQDKDVIAINQDPLGKQGYQLRQGDNFEVWERPLSGLAWA |
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| + | VAMINRQEIGGPRSYTIAVASLGKGVACNPACFITQLLPVKRKLGFYEWTSRLRSHINPTGTVLLQLENT |
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| + | MQMSLKDLL |
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== Sequence searches == |
== Sequence searches == |
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Revision as of 16:34, 3 May 2012
Please see Task 2 Results for our results on this topic.
Contents
Reference sequence
The reference sequence of α-Galactosidase A that will be used in the following tasks was obtained from Swissprot P06280.
>gi|4504009|ref|NP_000160.1| alpha-galactosidase A precursor [Homo sapiens] MQLRNPELHLGCALALRFLALVSWDIPGARALDNGLARTPTMGWLHWERFMCNLDCQEEPDSCISEKLFM EMAELMVSEGWKDAGYEYLCIDDCWMAPQRDSEGRLQADPQRFPHGIRQLANYVHSKGLKLGIYADVGNK TCAGFPGSFGYYDIDAQTFADWGVDLLKFDGCYCDSLENLADGYKHMSLALNRTGRSIVYSCEWPLYMWP FQKPNYTEIRQYCNHWRNFADIDDSWKSIKSILDWTSFNQERIVDVAGPGGWNDPDMLVIGNFGLSWNQQ VTQMALWAIMAAPLFMSNDLRHISPQAKALLQDKDVIAINQDPLGKQGYQLRQGDNFEVWERPLSGLAWA VAMINRQEIGGPRSYTIAVASLGKGVACNPACFITQLLPVKRKLGFYEWTSRLRSHINPTGTVLLQLENT MQMSLKDLL
Sequence searches
Blast
We searched the "big80" database with Blast with the following command:
blastall -p blastp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P06280.fasta -m 0 -o blastsearch_default.out -v 700 -b 700
The run took about 2 minutes (see section Time)
Psi-Blast
Iterations: 2 Evalue: 0.002 real 3m30.256s user 2m58.070s sys 0m13.360s Iterations: 2 Evalue: 0.000000001 real 3m8.507s user 3m5.180s sys 0m2.400s Iterations: 2 Evalue: 0.0000000001 real 3m10.271s user 3m7.620s sys 0m2.190s Iterations: 10 Evalue: 0.002 real 15m29.218s user 15m8.910s sys 0m12.730s Iterations: 10 Evalue: 0.000000001 real 16m33.748s user 16m12.500s sys 0m13.080s Iterations: 10 Evalue: 0.0000000001 real 16m20.137s user 15m55.910s sys 0m13.190s
HHblits / HHsearch
We searched the "big80" database with HHblits with the following command:
hhblits -i ../P06280.fasta -d /mnt/project/pracstrucfunc12/data/hhblits/uniprot20_current -e 0.003 -o hhblits_default.out -E 0.003 -Ofas hhblits_msa_default.txt -z 700 &
The run took about 2.5 minutes (see section Time)
Also, we ran HHblits with 8 iterations, instead of the preset 2. This took 14 minutes.
hhblits -i ~/Desktop/P06280.fasta -d /mnt/project/pracstrucfunc12/data/hhblits/uniprot20_current -e 0.003 -o hhblits_default_n8.out -E 0.003 -n 8
Time
We evaluated the time the programs ran with the command "time"
| Method | Parameter | Time |
|---|---|---|
| Blast v = 700 | b = 700, v = 700 | 1m53.944s |
| HHBlits | default | 2m19.519s |
| HHBlits | n = 8 | 13m49.545s |
