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

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(Comparison)
(Time)
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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]]).
 
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]]).
   
== Time ==
 
We evaluated the time the programs ran with the command "time"
 
   
  +
== Comparison ==
 
{|style="border-collapse: separate; border-spacing: 0; border-width: 1px; border-style: solid; border-color: #000; padding: 0; align: center; " width="85%"
 
! style="border-style: solid; border-width: 0 1px 1px 0"| Method
 
! style="border-style: solid; border-width: 0 1px 1px 0"| Parameter
 
! style="border-style: solid; border-width: 0 1px 1px 0"| Time
 
|-
 
| style="border-style: solid; border-width: 0 1px 1px 0"| Blast v = 700
 
| style="border-style: solid; border-width: 0 1px 1px 0"| b = 700, v = 700
 
| style="border-style: solid; border-width: 0 1px 1px 0"| 1m53.944s
 
|-
 
| style="border-style: solid; border-width: 0 1px 1px 0"| HHBlits
 
| style="border-style: solid; border-width: 0 1px 1px 0"| default
 
| style="border-style: solid; border-width: 0 1px 1px 0"| 2m19.519s
 
|-
 
| style="border-style: solid; border-width: 0 1px 1px 0"| HHBlits
 
| style="border-style: solid; border-width: 0 1px 1px 0"| n = 8
 
| style="border-style: solid; border-width: 0 1px 1px 0"| 16m7.754s
 
|}
 
 
=== Comparison ===
 
 
>R CMD BATCH all_Evalues.R
 
>R CMD BATCH all_Evalues.R

Revision as of 07:41, 5 May 2012

Please see Task 2 Results for our results on this topic. Please see also Task 2 Scripts for the used scripts.


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
./extract_ids_blast.sh blastsearch_default.out
perl ../download-annotation.pl blastsearch_default_ids.txt
perl ../compare_GO_terms.pl P06280 blastsearch_default_ids_GOterms.tsv
perl parse_blast.pl blastsearch_default.out


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
perl ../download-annotation.pl hhblits_default_ids.txt
perl ../compare_GO_terms.pl P06280 hhblits_default_ids_GOterms.tsv
perl parse_hhblits.pl hhblits_default.out

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 800 -b 800
./extract_ids_hhblits.sh hhblits_n8_neu.out
perl ../download-annotation.pl hhblits_n8_neu_ids.txt
perl ../compare_GO_terms.pl P06280 hhblits_n8_neu_ids_GOterms.tsv
perl parse_hhblits.pl hhblits_n8_neu.out

R CMD BATCH hist_hhblits.R

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


Comparison

  >R CMD BATCH all_Evalues.R