MAS help

A Multiple Sequence Alignment Program

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Transformation table:


OBJECTIVE ( object.tbl )
::::::::::::::
A-CDEFGHI-KLMN-PQRST-VW-Y-
A-CDEFGHI-KLMN-PQRST-VW-Y-

Use this for objective alignments


HYDROPHOBE ( hydro.tbl )
::::::::::::::
A-CDEFGHI-KLMN-PQRST-VW-Y-
B-BAABBAB-ABBC-BCACC-BB-B-

Use this for sequence tarnsformation based on hydrophobicity


MEMBRANE ( membrane.tbl )
::::::::::::::
A-CDEFGHI-KLMN-PQRST-VW-Y-
I-IOOINOI-OIIO-NOONN-IN-N-

To take into account wether the residues belong to a transmembrane segment


STRUCTURE ( struct.tbl )
::::::::::::::
A-CDEFGHI-KLMN-PQRST-VW-Y-
H-ECDBTDB-DAAT-TBDTE-BB-E-

For transformation based on secondary structure preference

Back
Minimum length of an anchor:

The length that a conserved oligopeptide must have, in order to be an anchor. Must be at least one (1), and at most the shortest sequence length minus two.

Back
Gap penalty:

Small values can lead to long alignments and insertion of many 'gaps'. The recommended range is between 5 and 50.

Back
Objective alignment:

If you choose Yes, the alignment between the anchors will be based on the original (not transformed sequence).

Transformation table:

Back
Minimum length of an anchor:

Back
Gap penalty:

Back
Objective alignment:

Back
Minimum length of an obligatory anchor:

Back
Optimization of the between anchor alignment:

Back
Print transformed sequences:

Back

Transformation table:

Back Minimum length of an anchor:

Back Gap penalty:

Back Objective alignment:

Back Minimum length of an obligatory anchor:

Back Optimization of the between anchor alignment:

Back Print transformed sequences:

Back

Back
Minimum length of an anchor:

Back
Gap penalty:

Back
Objective alignment:

Back
Minimum length of an obligatory anchor:

Back
Optimization of the between anchor alignment:

Back
Print transformed sequences: