Multiple Sequence Alignments

Multiple sequence alignments can be constructed in the following ways.

• Align the sequences of a set of orthologs by visiting the gene page for one of the genes, clicking the right-sidebar menu item Align Gene Nucleotide Sequence with Orthologs (or Align Gene Product Amino Acid Sequence with Orthologs), and selecting the organisms from which orthologs should be obtained. The alignment will be computed by Clustal Omega.
• Construct a SmartTable containing the genes or proteins you wish to align, then run one of the following commands from the right-sidebar menu for that SmartTable: Column → View Alignment of Gene Nucleotide Sequences or Column → View Alignment of Gene Product Peptide Sequences. The alignment will be computed by Clustal Omega.
• Align a set of arbitrary nucleotide sequence regions and optional other nucleotide sequences by entering the organism and start/end coordinates for each sequence region into the form created by clicking this button. To add the coordinates for a particular gene, search for the gene and then click the plus icon to insert the gene start and/or end coordinates with optional upstream or downstream offsets.

  Enter Nucleotide Sequence Regions

• Align a set of arbitrary proteins and optional other protein sequences by entering the organism and gene for each protein into the form created by clicking this button.

  Enter Proteins

• This page enables you to import a set of aligned sequences directly into the MSAviewer tool using the Import button below.

  Note that if you import unaligned sequences directly (e.g., FASTA file) then no aligner will be run. To import a set of aligned sequences, use Clustal or FASTA format.

For more information on how to build sequence alignments in BioCyc, see the Website User's Guide.