Difference between revisions of "Fabry:Sequence alignments (sequence searches and multiple alignments)/Journal"

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=== HHblits / HHsearch ===
  
=== HHblits / HHsearch ===
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We searched the "big80" database with HHblits with the following command:
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We searched the "big80" database with HHblits using the default settings and also with the maximum number of possible iterations (8) with the following commands:
   
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<code>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 </code>
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<code>time hhblits -i ../P06280.fasta -d /mnt/project/pracstrucfunc12/data/hhblits/uniprot20_current -e 0.003 -o hhblits_default.out -E 0.003 -z 700
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./extract_ids_hhblits.sh hhblits_default.out
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./extract_evalues_hhblits.pl hhblits_default.out
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perl ../download-annotation.pl hhblits_default_ids.txt
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perl ../compare_GO_terms.pl P06280 hhblits_default_ids_GOterms.tsv
   
  +
time hhblits -i ../P06280.fasta -d /mnt/project/pracstrucfunc12/data/hhblits/uniprot20_current -e 0.003 -o hhblits_n8_neu.out -E 0.003 -n 8 -z 1500
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The run took about 2.5 minutes (see section [[Sequence_alignments_(sequence_searches_and_multiple_alignments)#Time | Time]])
  
  +
./extract_ids_hhblits.sh hhblits_n8.out
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./extract_evalues_hhblits.pl hhblits_n8.out
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perl ../download-annotation.pl hhblits_n8_ids.txt
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perl ../compare_GO_terms.pl P06280 hhblits_n8_ids_GOterms.tsv
   
  +
R CMD BATCH hist_hhblits.R </code>
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Also, we ran HHblits with 8 iterations, instead of the preset 2. This took 14 minutes.
  
   
  +
The first HHblits run took about 2.5 minutes, the second one about 16 minutes (see section [[Sequence_alignments_(sequence_searches_and_multiple_alignments)#Time | Time]]).
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<code>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</code>
  
   
 
== Time ==
  
== Time ==

Revision as of 21:29, 3 May 2012

Please see Task 2 Results for our results on this topic.

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 using the default settings and also with the maximum number of possible iterations (8) with the following commands:

time hhblits -i ../P06280.fasta -d /mnt/project/pracstrucfunc12/data/hhblits/uniprot20_current -e 0.003 -o hhblits_default.out -E 0.003 -z 700 ./extract_ids_hhblits.sh hhblits_default.out ./extract_evalues_hhblits.pl hhblits_default.out perl ../download-annotation.pl hhblits_default_ids.txt perl ../compare_GO_terms.pl P06280 hhblits_default_ids_GOterms.tsv

time hhblits -i ../P06280.fasta -d /mnt/project/pracstrucfunc12/data/hhblits/uniprot20_current -e 0.003 -o hhblits_n8_neu.out -E 0.003 -n 8 -z 1500 ./extract_ids_hhblits.sh hhblits_n8.out ./extract_evalues_hhblits.pl hhblits_n8.out perl ../download-annotation.pl hhblits_n8_ids.txt perl ../compare_GO_terms.pl P06280 hhblits_n8_ids_GOterms.tsv

R CMD BATCH hist_hhblits.R

The first HHblits run took about 2.5 minutes, the second one about 16 minutes (see section Time).

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
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