Glucocerebrosidase sequence alignments

Sequence searches

Fasta

Fasta was not yet installed, so we downloaded it here: [[1]]
../bin/fasta36 gbaseq.fasta /data/blast/nr/nr > fasta_gba_search.out

identity	percentage	number
>= 0%	0.0	0
>= 10%	0.0	0
>= 20%	0.462	240
>= 30%	0.308	160
>= 40%	0.085	44
>= 50%	0.012	6
>= 60%	0.006	3
>= 70%	0.012	6
>= 80%	0.052	27
>= 90%	0.065	34
Total: 520

Blast

blastall -p blastp -d /data/blast/nr/nr -i gbaseq.fasta -o blast.out

identity	percentage	number
>= 0%	0.0	0
>= 10%	0.0	0
>= 20%	0.172	43
>= 30%	0.508	127
>= 40%	0.112	28
>= 50%	0.024	6
>= 60%	0.012	3
>= 70%	0.004	1
>= 80%	0.06	15
>= 90%	0.108	27
Total: 250

PSI-Blast

3 iterations, E-value cutoff 0.005

blastpgp -d /data/blast/nr/nr -i gbaseq.fasta -o psi_blast_3_0.005.out -j 3 -h 0.005

identity	percentage	number
>= 0%	0.0	0
>= 10%	0.0	0
>= 20%	0.34	85
>= 30%	0.392	98
>= 40%	0.104	26
>= 50%	0.016	4
>= 60%	0.0	0
>= 70%	0.004	1
>= 80%	0.036	9
>= 90%	0.108	27
Total: 250

3 iterations, E-value cutoff 10E-6

blastpgp -d /data/blast/nr/nr -i gbaseq.fasta -o psi_blast_3_10E-6.out -j 3 -h 10E-6

identity	percentage	number
>= 0%	0.0	0
>= 10%	0.0	0
>= 20%	0.34	85
>= 30%	0.392	98
>= 40%	0.104	26
>= 50%	0.016	4
>= 60%	0.0	0
>= 70%	0.004	1
>= 80%	0.036	9
>= 90%	0.108	27
Total: 250

5 iterations, E-value cutoff 0.005

blastpgp -d /data/blast/nr/nr -i gbaseq.fasta -o psi_blast_5_0.005.out -j 5 -h 0.005

identity	percentage	number
>= 0%	0.0	0
>= 10%	0.0	0
>= 20%	0.384	96
>= 30%	0.36	90
>= 40%	0.096	24
>= 50%	0.012	3
>= 60%	0.0	0
>= 70%	0.004	1
>= 80%	0.036	9
>= 90%	0.108	27
Total: 250

5 iterations, E-value cutoff 10E-6

blastpgp -d /data/blast/nr/nr -i gbaseq.fasta -o psi_blast_5_10E-6.out -j 5 -h 10E-6

identity	percentage	number
>= 0%	0.0	0
>= 10%	0.0	0
>= 20%	0.376	94
>= 30%	0.364	91
>= 40%	0.1	25
>= 50%	0.012	3
>= 60%	0.0	0
>= 70%	0.004	1
>= 80%	0.036	9
>= 90%	0.108	27
Total: 250

HHSearch

For HHSearch we used [[2]] with the pdb70 database of May 14th.

Multiple sequence alignments

Cobalt

Cobalt was not yet installed, so we downloaded it here: [[3]]

time /home/student/Desktop/ncbi-cobalt-2.0.1/cobalt -i multiple_alignment.fasta -norps T > cobalt_multiple_alignment.aln

	time
real	0m3.488s
user	0m2.320s
sys	0m0.180s

ClustalW

time clustalw

	time
real	0m40.625s
user	0m5.320s
sys	0m0.070s

Muscle

time muscle -in multiple_alignment.fasta -out muscle_multiple_alignment.aln

	time
real	0m3.018s
user	0m1.710s
sys	0m0.100s

T-Coffee

time t_coffee multiple_alignment.fasta

	time
real	0m41.360s
user	0m34.000s
sys	0m0.920s

3D-Coffee/Expresso

time t_coffee -seq multiple_alignment.fasta -mode expresso -pdb_type dn

	time
real	12m19.825s
user	5m17.140s
sys	0m46.970s