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Sequence to Sequence Alignment
Align Two Multiple Sequence Alignments
AlignMe FAQ
Run AlignMe in MSAMSA mode
1. Provide sequences
This form allows you to align two averaged multiple sequence alignments. You have two provide one or more sequences that are aligned to one another. All sequences within an alignment have to be in fasta format and must have the same length, including gaps.
Enter a multiple sequence alignment
with sequences in fasta format
Enter a multiple sequence alignment
with sequences in fasta format
...or upload a fasta file
...or upload another fasta file
ERROR: Enter 2 multiple sequence alignments with sequences in fasta format
ERROR: First sequence missing  please upload a fastafile or paste a sequence
ERROR: Second sequence missing  please upload a fastafile or paste a sequence
ERROR: Please choose a first fastafile for uploading
ERROR: Please choose a second fastafile for uploading
ERROR: If you want to upload a first fastafile please select the corresponding checkbox
ERROR: If you want to upload a second fastafile please select the corresponding checkbox
ERROR Sequence1: The inputsequence has to be in fastaformat
ERROR Sequence2: The inputsequence has to be in fastaformat
2. Select optimized or userdefined parameters
Gap penalties have been systematically tested on fivetransmembrane helix repeat sequences using the HWvH hydrophobicity scale with a triangular sliding window of size 13 and the fraction of allowed gaps set to 0.5.
Parameters for αhelical membrane proteins
fast (~3 seconds)
based on substitution matrix & hydrophobicity scale
Or use your own alignment parameters
Define your own parameters
ERROR: You have to select a type of alignment parameters for your alignment!
Hide detailed alignment parameter options
Show detailed alignment parameter options
2.1. Gap penalties
AlignMe uses a NeedlemanWunsch algorithm with an affine gap penalty scheme. Gap penalties define how likely amino acids are to be aligned with one another or against a gap.
In general, affine gap penalties have a gap opening penalty (o) and a gap extension penalty (e). A gap of length n is then given a score of: o + (n1)e. All gap penalties have to be positive integers or fractions (no commas).
AlignMe allows you to define either 2, 4 or 6 gap penalties:
2: A gap open penalty and a gap extension penalty are used along the entire length of the sequence.
4: Special gap penalties can be assigned to gaps at the end of the alignment (N or Cterminal gaps). This can be useful if gaps are more (or less) likely to appear at the termini than within the sequence. Thus the third and fourth parameters are the gap open and gap extension penalities of the terminal gaps.
6: By using 6 gap penalties and a threshold value it is possible to subdivide the sequence into 2 different subsets to which different gap penalties are assigned. Subset 1: below threshold gap opening and extension penalty (first & second params) Subset 2: above threshold gap opening and extension penalty (third & fourth params) The fifth & sixth parameters are the gap open and gap extension penalities of the terminal gaps.
Select number of gap penalties:
2
4
6
ERROR: Please choose gap penalties!!
Gap opening penalty
Gap extension penalty
ERROR: Please enter a gap opening penalty
ERROR: Format of gap opening penalty incorrect  positive integers or fractions only (no commas)
ERROR: Please enter a gap extension penalty
ERROR: Format of gap extension penalty incorrect  positive integers or fractions only (no commas)
Gap opening penalty
Gap extension penalty
Terminal gap opening penalty
Terminal gap extension penalty
ERROR: Please enter a gap opening penalty
ERROR: Format of gap opening penalty incorrect  positive integers or fractions only (no commas)
ERROR: Please enter a gap extension penalty
ERROR: Format of gap extension penalty incorrect  positive integers or fractions only (no commas)
ERROR: Please enter a gap opening penalty for the termini
ERROR: Format of terminal gap open penalty incorrect  positive integers or fractions only (no commas)
ERROR: Please enter a gap extension penalty for the termini
ERROR: Format of terminal gap extension penalty incorrect  positive integers or fractions only (no commas)
Below threshold gap opening penalty
Below threshold gap extension penalty
Above threshold gap opening penalty
Above threshold gap extension penalty
Terminal gap opening penalty
Terminal gap extension penalty
ERROR: Please enter a minimum gap open penalty
ERROR: Format of minimum gap open penalty incorrect  positive integers or fractions only (no commas)
ERROR: Please enter a minimum gap extension penalty
ERROR: Format of minimum gap extension penalty incorrect  positive integers or fractions only (no commas)
ERROR: Please enter a maximum gap open penalty
ERROR: Format of maximum gap open penalty incorrect  positive integers or fractions only (no commas)
ERROR: Please enter a maximum gap extension penalty
ERROR: Format of maximum gap extension penalty incorrect  positive integers or fractions only (no commas)
ERROR: Please enter a termini gap open penalty
ERROR: Format of termini gap open penalty incorrect  positive integers or fractions only (no commas)
ERROR: Please enter a termini gap extension penalty
ERROR: Format of termini gap extension penalty incorrect  positive integers or fractions only (no commas)
2.2. Scales
Hydrophobicity scales assign a relative hydrophobicity to a certain amino acid. These values are obtained by experimental theoretical or combined approaches. A scale should look like this:
A 1.80 C 2.50 D 3.50 E 3.50 . .... . ....
This example shows an excerpt of the KyteDoolittle scale.
It is possible to smooth the hydrophobicity profile with 4 different types of window averaging: triangular, rectangular, sinusoidal and zigzag. The size of the window must also be provided. Detailed information about window types is provided in the manual.
Scale
Upload a custom scale
Window type
Size
Weight
Use?
Threshold
Select a scale:
Upload custom scale
EW (Eisenberg & Weiss)
HWvH (Hessa, White & von Heinje)
KD (Kyte & Doolittle)
WW (Wimley & White)
Select a window type:
none
triangular
ERROR in input line 1: Please enter a weight
ERROR in input line 1: Format of weight is incorrect  positive integers or fractions only (no commas)
ERROR in input line 1: Please select a scale
ERROR in input line 1: Please choose a scale to upload
ERROR in input line 1: Please select a window type
ERROR in input line 1: Please enter a window size
ERROR in input line 1: Format of window size is incorrect  positive integers except 0 (no commas)
ERROR in input line 1: Please enter a threshold value
ERROR in input line 1: Format of threshold value is incorrect  integers or fractions only (no commas)
ERROR: Please enter at least one input (profile, scale or matrix) before submitting a job
ERROR: A threshold has to be set!
Allowed fraction of gaps
For each position in the multiple sequence alignment an average hydrophobicity value is calculated. Therefore each column of the multiple sequence alignment is checked for the fraction of gaps that it contains.
If the fraction of gaps in a given column is higher than the threshold value that the user has set, this column will not be considered in the alignment.
Example:
Fraction of gaps threshold = 0.5
> columns in which more than 50 % of all positions are gaps are skipped and not considered in the alignment.
ERROR: Please enter a number
ERROR: Format of gapfraction is incorrect  positive integers or fractions only (no commas).
3. Submit
Submission failed!
Please see the error messages displayed above on this page,
change the inputs accordingly, and resubmit.
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