Glucocerebrosidase sequence alignments
From Bioinformatikpedia
Revision as of 09:08, 21 May 2011 by Brunners (talk | contribs) (New page: == Sequence searches == === Fasta === Fasta was not yet installed, so we downloaded it here: ftp://ftp.ebi.ac.uk/pub/software/unix/fasta/fasta36/<br/> <code>../bin/fasta36 gbaseq.fast...)
Contents
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]] of the Bioinformatics Toolkit of the gene center width the pdb70 database of May 14th.
