Protein sequence description |
Description of your single input protein sequence. Setting is optional. A description text longer than 100 chars will be abbreviated. |
Searched position |
Here you can prove the conservation for a particular position of your single query sequence.
Be sure that at your set position is located the searched amino acid for which you want to calculate the conservation.
The pipeline is iterating maximal 9 times to get an optimized amino acid score for the amino acid on set position.
Set 0 if programm should calculate conservation for all found given amino acids. Default is 0.
Maximum is 10,000 because query length higher than 10,000 is not allowed. |
Maximal count of BLAST results |
Maximal count of complete BLAST results which will be looked for filtering.
Boundary is 500<= VALUE <=100000. Default is 20000. |
BLAST E-Value threshold |
E-Value threshold for BLAST results.
Boundary is 0.0< VALUE <=10.0. Default is 0.0000000001 or rather 1E-10 |
Gap open penalty |
Gap open penalty for multiple alignment.
Boundary is 1< VALUE <=100. Default is 12. |
Gap extension penalty |
Gap extension penalty for multiple alignment.
Boundary is 1< VALUE <=100. Default is 1. |
Amino acid score threshold |
Threshold for amino acid score
-> the amino acid in query is probably conserved when the amino acid score is higher than the given threshold.
Boundary is 0.1<= VALUE <=0.9. Default is 0.5. |
P-Value threshold |
Threshold for P-Value
-> the amino acid in query is probably conserved when the amino acid's corresponding P-Value is lower than the given threshold.
Boundary is 0.1<= VALUE <=0.9. Default is 0.5. |
Searched amino acid |
Searched amino acid for calculating the conservation.
Available amino acids are cysteine, tryptophan, serine, threonine, tyrosine and methionine.
The search is limited to these because they are more of a functional role in the organism cell.
Default is cysteine. |
Substitution BLOSUM matrix |
Substitution matrix (BLOSUM matrix) for multiple alignment. You can choose from blosum30 to blosum100.
Lower matrix is used for sequences where lower similarity between them is expected, higher matrix is for higher similarity expected.
Default matrix is blosum62. |