AlignMe

Run AlignMe in MSA-MSA 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

2. Select optimized or user-defined parameters
Gap penalties have been systematically tested on five-transmembrane 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 α-helical membrane proteins

fast (~3 seconds)
based on substitution matrix & hydrophobicity scale

Or use your own alignment parameters

Define your own parameters

Show detailed alignment parameter options

2.1. Gap penalties
AlignMe uses a Needleman-Wunsch 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 + (n-1)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 C-terminal 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

Gap opening penalty

Gap extension penalty

Gap opening penalty		Gap extension penalty
Terminal gap opening penalty		Terminal gap extension penalty

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

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:

This example shows an excerpt of the Kyte-Doolittle 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

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.

3. Submit

Enter an e-mail address to receive a message containing your results (not required)

AlignMe

Run AlignMe in MSA-MSA 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.

...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 fasta-file or paste a sequence

ERROR: Second sequence missing - please upload a fasta-file 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 input-sequence has to be in fasta-format

ERROR Sequence2: The input-sequence has to be in fasta-format

2. Select optimized or user-defined parameters Gap penalties have been systematically tested on five-transmembrane 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 α-helical membrane proteins

Or use your own alignment parameters

ERROR: You have to select a type of alignment parameters for your alignment!

ERROR: Please choose gap penalties!!

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

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)

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)

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!

ERROR: Please enter a number

ERROR: Format of gap-fraction 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.

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.

2. Select optimized or user-defined parameters
Gap penalties have been systematically tested on five-transmembrane 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.

Submission failed!
Please see the error messages displayed above on this page,
change the inputs accordingly, and resubmit.