Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment

Abstract

Obtaining high quality multiple alignments is crucial for a range of sequence analysis tasks. A common strategy is to align the sequences several times, varying the program or parameters until the best alignment according to manual inspection by human experts is found. Ideally, this should be assisted by an automatic assessment of the alignment quality. Our web-site http://msa.cgb.ki.se allows users to perform all these steps: Kalign to align sequences, Kalignvu to view and verify the resulting alignments and Mumsa to assess the quality. Due to the computational efficiency of Kalign we can allow users to submit hundreds of sequences to be aligned and still guarantee fast response times. All servers are freely accessible and the underlying software can be freely downloaded for local use.

Figure 1

Alignments viewed by Kalignvu with different color schemes and font sizes. (A) Balibase reference alignment ‘BB30002’ with the default conservation scheme. (B) An alignment of odorant receptors colored by the hydrophobicity colour scheme (window length of 21). Kalignvu implements a scale from blue to red in nine steps corresponding to the minimum–maximum hydrophobicity. Here, the red segments indicate transmembrane domains and the blue segments an interconnecting hydrophilic loop. Note that most gaps occur within the hydrophilic loops. (C) Balibase reference alignment ‘BB30014’ with Pfam domains ‘PF00043’ and ‘PF02798’ highlighted.