Using Ref sequence in "Assemble in Groups"

[jt-umdnj]

Hi,
I've been trying to align a set of sequences to a reference sequence using "Assemble in Groups", but I can't get it to work the way it does in the online tutorial. I've used "Make Reference Sequence" to designate the reference sequence. I've tried both 1) selecting the unassembled sequence folder then doing assemble in groups and 2) selecting the whole set of sequences, including the reference, then doing assemble in groups. In both cases, the contigs are formed in groups, but the reference sequence is ignored; the contigs wind up in different orientations. Any idea what I might be doing wrong? I'm using version 4.0.4
Thanks,
Jim

[Nina Schweikardt]

Hi Jim,

To align sequences to a reference sequence please use "Align in Groups" instead of "Assemble in Groups". This feature is available from the "Contig" menu -> "Advanced Alignments" -> "Align in Groups...". Assemblies are generated without a reference sequence in CodonCode Aligner, alignments use a references sequence.

Please note also that there are two different preference panels for alignments and assemblies if you change the assembly / alignment parameters.