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

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== Multiple sequence alignments ==
 
== Multiple sequence alignments ==
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=== Results ===
 
The following commands were used to generate the multiple sequence alignments. The pictures were obtained by using jalview
 
The following commands were used to generate the multiple sequence alignments. The pictures were obtained by using jalview
   
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/mnt/opt/T-Coffee/bin/t_coffee -seq fabry_dataset_59.fasta -outfile msa/tcoffee_fabry_dataset_59.msa &
 
/mnt/opt/T-Coffee/bin/t_coffee -seq fabry_dataset_59.fasta -outfile msa/tcoffee_fabry_dataset_59.msa &
 
/mnt/opt/T-Coffee/bin/t_coffee -seq fabry_dataset_39.fasta -outfile msa/tcoffee_fabry_dataset_39.msa &
 
/mnt/opt/T-Coffee/bin/t_coffee -seq fabry_dataset_39.fasta -outfile msa/tcoffee_fabry_dataset_39.msa &
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The number of gaps were counted with the perl script "countGaps.pl".

Revision as of 09:42, 6 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


Multiple sequence alignments

Results

The following commands were used to generate the multiple sequence alignments. The pictures were obtained by using jalview

clustalw -infile=fabry_dataset_99.fasta -outfile=msa/clustalw_fabry_dataset_99.msa &
clustalw -infile=fabry_dataset_89.fasta -outfile=msa/clustalw_fabry_dataset_89.msa &
clustalw -infile=fabry_dataset_59.fasta -outfile=msa/clustalw_fabry_dataset_59.msa &
clustalw -infile=fabry_dataset_39.fasta -outfile=msa/clustalw_fabry_dataset_39.msa &

muscle -in fabry_dataset_99.fasta -out msa/muscle_fabry_dataset_99.msa &
muscle -in fabry_dataset_89.fasta -out msa/muscle_fabry_dataset_89.msa &
muscle -in fabry_dataset_59.fasta -out msa/muscle_fabry_dataset_59.msa &
muscle -in fabry_dataset_39.fasta -out msa/muscle_fabry_dataset_39.msa &

/mnt/opt/T-Coffee/bin/t_coffee -seq fabry_dataset_99.fasta  -outfile msa/tcoffee_fabry_dataset_99.msa  &
/mnt/opt/T-Coffee/bin/t_coffee -seq fabry_dataset_89.fasta  -outfile msa/tcoffee_fabry_dataset_89.msa  &
/mnt/opt/T-Coffee/bin/t_coffee -seq fabry_dataset_59.fasta  -outfile msa/tcoffee_fabry_dataset_59.msa  &
/mnt/opt/T-Coffee/bin/t_coffee -seq fabry_dataset_39.fasta  -outfile msa/tcoffee_fabry_dataset_39.msa  &

The number of gaps were counted with the perl script "countGaps.pl".