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SuiteMSA: visual tools for multiple sequence alignment comparison and molecular sequence simulation

Catherine L Anderson1, Cory L Strope2 and Etsuko N Moriyama23*

Author Affiliations

1 Department of Computer Science and Engineering, University of Nebraska, Lincoln, Nebraska 68588, USA

2 School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588, USA

3 Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska 68588, USA

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BMC Bioinformatics 2011, 12:184  doi:10.1186/1471-2105-12-184

Published: 21 May 2011

Additional files

Additional file 1:

23 lipocalin protein sequences. The 23 lipocalin protein sequences obtained from Sánchez et al. [27] are included in fasta format.

Format: TXT Size: 4KB Download file

Open Data

Additional file 2:

The reference alignment of 23 lipocalin proteins. The alignment of the 23 lipocalin protein sequences obtained from Sánchez et al. [27] is included in fasta format.

Format: TXT Size: 5KB Download file

Open Data

Additional file 3:

The phylogenetic tree of 23 lipocalin proteins. The phylogenetic tree of the 23 lipocalin protein sequences obtained from Sánchez et al. [27] is included in Newick format.

Format: TXT Size: 1KB Download file

Open Data

Additional file 4:

Secondary structure predictions for 23 lipocalin proteins. The secondary structures for the 23 lipocalin proteins predicted by PSIPRED are provided in fasta format.

Format: TXT Size: 4KB Download file

Open Data

Additional file 5:

The guide tree file. File name: lipocalinSuperfamily.tree. This file contains the guide tree along with other parameters used for the iSGv2.1 simulation of the lipocalin superfamily proteins. In addition to this file, Additional files 6-8 are used for the simulation. A brief instruction for setting up SuiteMSA using these files and running the simulation as described in the case study is included in the SuiteMSA package distribution.

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Additional file 6:

The simulation root MSA. File name: lipocalinSuperfamily_template.maroot. This file contains the multiple sequence alignment along with the patterns for the motif and template used for the lipocalin superfamily simulation.

Format: TXT Size: 6KB Download file

Open Data

Additional file 7:

The lineage specification file. File name: lipocalinSuperfamily.spec. This file contains the motif specifications for lineages used for the lipocalin superfamily simulation.

Format: TXT Size: 1KB Download file

Open Data

Additional file 8:

The indel-length distribution file. File name: lipocalin.idlen. This file contains the indel-length distribution used for the lipocalin superfamily simulation.

Format: TXT Size: 1KB Download file

Open Data