Difference between revisions of "Gaucher Disease: Task 02 - Alignments"
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Kalemanovm (talk | contribs) (→Pairwise Sequence Alignment) |
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==Theoretical Background== |
==Theoretical Background== |
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| − | == |
+ | ==Sequence Searches== |
| + | Sequence searches with our query protein sequence, P04062.fasta, were done with the following programs: |
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| + | * '''BLAST''' |
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| − | ===Blast=== |
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| + | ** using standard parameters |
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| + | ** against big80 |
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| + | * '''Psi-BLAST''' |
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| − | ===PSI-Blast=== |
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| + | ** with number of shown hits and alignments set to 10000 (-b, -v options) |
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| + | ** with all combinations of: |
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| + | *** 2 iterations: 1 iterations against big_80 followed by 1 iteration against big |
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| + | *** 10 iterations: 9 iterations against big_80 followed by 1 iteration against big |
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| + | *** default E-value cutoff (0.002) |
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| + | *** E-value cutoff 10E-10 |
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| + | ** other options leaved default |
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| + | * '''HHblits''' |
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| − | ===HHBlits=== |
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| + | ** with number of shown hits and alignments set to 10000 (-b, -v options) |
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| + | ** with all combinations of: |
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| + | *** 2 iterations against uniprot_20 |
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| + | *** 10 iterations against uniprot_20 |
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| + | *** default E-value cutoff (0.002) |
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| + | *** E-value cutoff 10E-10 |
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| + | ** other options leaved default |
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| + | |||
| + | The script [[run.pl]] was written and used for the runs. PSSM files - a3m and hhr for HHblits, chk ("checkpoint") and PSSM for Psi-BLAST were created in order to start the search against another database, from big_80 to big for Psi-BLAST and later against a PDB database for the evaluation. |
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| + | |||
| + | ===Comparison=== |
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===Evaluation=== |
===Evaluation=== |
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Revision as of 20:51, 5 May 2013
Alignments allow a comparisons of Strings. In the field of bioinformatics, sequence alignments show the relation between two or more sequences.
Contents
Theoretical Background
Sequence Searches
Sequence searches with our query protein sequence, P04062.fasta, were done with the following programs:
- BLAST
- using standard parameters
- against big80
- Psi-BLAST
- with number of shown hits and alignments set to 10000 (-b, -v options)
- with all combinations of:
- 2 iterations: 1 iterations against big_80 followed by 1 iteration against big
- 10 iterations: 9 iterations against big_80 followed by 1 iteration against big
- default E-value cutoff (0.002)
- E-value cutoff 10E-10
- other options leaved default
- HHblits
- with number of shown hits and alignments set to 10000 (-b, -v options)
- with all combinations of:
- 2 iterations against uniprot_20
- 10 iterations against uniprot_20
- default E-value cutoff (0.002)
- E-value cutoff 10E-10
- other options leaved default
The script run.pl was written and used for the runs. PSSM files - a3m and hhr for HHblits, chk ("checkpoint") and PSSM for Psi-BLAST were created in order to start the search against another database, from big_80 to big for Psi-BLAST and later against a PDB database for the evaluation.
