| Goal 1 | To merge contigs into a pseudo-molecule with a 36 bp linker that introduces a stop codon (linker: NNNNNCACACACTTAATTAATTAAGTGTGTGNNNNN) in all six frames. |
|---|---|
| Script 1 | $linker="NNNNNCACACACTTAATTAATTAAGTGTGTGNNNNN" pseudo.fas=contig00001.fas+$linker+contig00002.fas |
| Goal 2 | After annotation or gene-finding via pseudo.gbk, break the pseudo-molecule back into contigs: contig00001 length=116581 contig00002 length=97153 You will need to determine the correct endpoints for the de-concatenation step, as SeqNinja cannot do this automatically. |
| Script 2 | contig00001.gbk=pseudo.gbk(1,116581) contig00002.gbk=pseudo.gbk(116618,213770) |
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