Multiple Sequence Alignments on the BAR

• Based on diverse Bioperl modules, ClustalW (v 2.1) and MView. Runs locally on the BAR.
• Simply paste sequences (Protein- or DNA- with or without line numbers) below, and give them names, or upload an MSF file.
• Then select the output options you desire.
• Then click Align ...results may be copied into Word 2000 or higher, and formatting will be retained.
• Sequence 1 should be the longest!

Enter Sequences in FASTA format below, and provide a name for the alignment (letters and _ or - only):

or Upload an Alignment File (MSF, Blast, FASTA etc.):

ClustalW Parameters ClustalW Help at the EBI (defaults selected)

for fast Protein Alignments

Output Format
Output Order
Ktup (word size)
Window Length
delay divergent seqs. <	%
Score Type
Top Diagonal
Pairgap
Matrix
Gap Open
Penalize End Gaps?
Gap Extension
Gap Distances

for fast DNA Alignments

Output Format
Output Order
Ktup (word size)
Window Length
delay divergent seqs. <	%
Score Type
Top Diagonal
Pairgap
Matrix
Gap Open
Penalize End Gaps?
Gap Extension
Gap Distances
Transition Weight

Output Options for MView MView FAQs | Index for MView

Ruler	On Off
Colour Mode	Any Identity Consensus Group
Threshold
Width of Blocks
Show Consensus	On Off
Consensus Colour Mode	Colourmaps
Consensus Threshold	Try also e.g. 80 or 60!
Consensus Display Mode	Single Class
Consensus calculation +/- Gaps	On Off
Consensus Reference Seq	According to name or number in MSF.

Desired Output Style:
fine-tune at bottom left...

black-gray-white (default)

black-white (Patent!)

coloured, according to property

Type: Protein DNA