2.6.5 Sequence Menu

This contains several operations for manipulating nucleotide and protein sequences, including processing NGS reads prior to assembly.

• New Sequence: Create a new nucleotide or protein sequence (including oligos) from residues that you can paste or type in. See section 5.1 .
• Extract Region: Extract the selected part of a sequence or alignment into a new document.
• Reverse Complement: Reverse sequence direction and replace each base by its complement. See section 5.5 .
• Translate: Creates a new protein document from the translated DNA, see section 5.6 .
• Back Translate: Creates nucleotide version of the selected protein document, see section 5.6.2 .
• Circular Sequences: Sets whether the currently selected sequences are circular. This effects the way the sequence view displays them as well as how certain operations deal with the sequences (eg. digestion). See section 5.2.3 .
• Free End Gaps Alignment: Sets whether the currently selected alignment has free end gaps. This effects calculation of the consensus sequences and statistics.
• Change Residue Numbering...: Changes the base numbering of the selected sequence. On a circular sequence this function can be used to shift the origin of the sequence to a different location. On a linear sequence this can be used to indicate that the sequence is a subsequence of a larger sequence; to number a sequence with respect to a particular location (ie make the start of a gene base 1); or to reverse the numbering of a sequence. This will introduce two numbering systems into your sequence: the original numbering (Standard), and the numbering that you have specified (Source).
• Convert between DNA and RNA: Changes all T’s in a sequence to U’s or vice versa, depending on the type of the selected sequence. Once this is performed, click “Save” in the Sequence View to make the change permanent.
• Set Read Direction: Marks sequences as forward or reverse reads so the correct reads are reverse complemented by assembly.
• Set Read Technology: Specifies the sequencing platform used to generate sequence reads. See section 10.1 .
• Set Paired Reads: Sets up paired reads for assembly. See section 10.2.1 .
• Merge Paired Reads: Merges paired reads using BBMerge, see section 10.2.3 .
• Remove Duplicate Reads: Uses Dedupe to remove duplicate sequences from NGS datasets, see section 10.2.4 .
• Error Correct and Normalize: Uses BBNorm to error correct and normalize NGS reads, see section 10.2.6 .
• Separate Reads by Barcode separates multiplex or barcode data (e.g. 454 MID data). See section 10.2.7
• Group Sequences into a List creates a sequence list containing copies of all of the selected sequences. See section 5.1.1 .
• Extract Sequence from List copies each sequence out of a sequence list into a separate sequence document.