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

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Please see also [[Fabry:Sequence_alignments_(sequence_searches_and_multiple_alignments):Scripts | Task 2 Scripts]] for the used scripts.
 
Please see also [[Fabry:Sequence_alignments_(sequence_searches_and_multiple_alignments):Scripts | Task 2 Scripts]] for the used scripts.
   
 
== Reference sequence ==
 
 
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].
 
 
>gi|4504009|ref|NP_000160.1| alpha-galactosidase A precursor [Homo sapiens]
 
MQLRNPELHLGCALALRFLALVSWDIPGARALDNGLARTPTMGWLHWERFMCNLDCQEEPDSCISEKLFM
 
EMAELMVSEGWKDAGYEYLCIDDCWMAPQRDSEGRLQADPQRFPHGIRQLANYVHSKGLKLGIYADVGNK
 
TCAGFPGSFGYYDIDAQTFADWGVDLLKFDGCYCDSLENLADGYKHMSLALNRTGRSIVYSCEWPLYMWP
 
FQKPNYTEIRQYCNHWRNFADIDDSWKSIKSILDWTSFNQERIVDVAGPGGWNDPDMLVIGNFGLSWNQQ
 
VTQMALWAIMAAPLFMSNDLRHISPQAKALLQDKDVIAINQDPLGKQGYQLRQGDNFEVWERPLSGLAWA
 
VAMINRQEIGGPRSYTIAVASLGKGVACNPACFITQLLPVKRKLGFYEWTSRLRSHINPTGTVLLQLENT
 
MQMSLKDLL
 
   
 
== Sequence searches ==
 
== Sequence searches ==
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perl parse_blast.pl blastsearch_default.out
 
perl parse_blast.pl blastsearch_default.out
   
 
The run took about 2 minutes (see section [[Sequence_alignments_(sequence_searches_and_multiple_alignments)#Time | Time]])
 
   
 
=== Psi-Blast ===
 
=== Psi-Blast ===
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R CMD BATCH hist_hhblits.R
 
R CMD BATCH hist_hhblits.R
 
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]]).
 
   
   

Revision as of 07:45, 5 May 2012

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


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


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


Comparison

Venn diagrams created with Oliveros, J.C. (2007) VENNY. An interactive tool for comparing lists with Venn Diagrams.

  >R CMD BATCH all_Evalues.R