- AA
- Abbreviation for amino acid.
- Consensus
- A sequence that was constructed from a contig, using a specific consensus caller.
- Contig
- The alignment of a set of reads and the thereof derived consensus. A contig can also just consists of a single read.
- Cropping
- A contig related “soft” cut of reads and consensus according to signuatures or ref.-seq. (as defined in the Task Tempalte). This operation is always reversible and will be redone when reassembling.
- Read
- A chromatogram or FASTA-like sequence that can be added to a target assembly. Several reads can be aligned into a contig.
- Database Scheme
- Defines which database fields should be used for samples. A Database Scheme may be assigned to one ore more Projects
- MBQ (mean base quality)
- The mean quality for all bases in the trimmed region.
- nt
- Abbreviation for nucleotide.
- ORF
- Open reading frame. A ref.-seq. layer can be set to one of the three possible ORFs: +0, +1, or +2
- Project
- A Project is a categorization for several Samples. It is defined by a Database Scheme and one or more Task Templates.
- ref.-seq.
- The Reference Sequence defined for each target of a Task Templates. The ref.-seq. may also be dynamically chosen from a sequence library.
- RT20, RT20ratio
- The RidomTracer (RT, a component of the software) assigns quality values to each base call in a chromatogram. RT20 defines the number of bases with a quality >= 20 in the trimmed trace region. RT20ratio gives the ratio of RT20 to the total number of bases in the trimmed trace region.
- Sequence
- Either a read or contig consensus DNA or protein sequence.
- Signature
- Sequence patterns that are searched for and marked in sequences. Can be used to trim sequences.
- Target
- A Task Entry contains one or more targets, defined by the associated Task Template. A target should contain only one contig.
- Target Parameters
- Each target has a set of Target Parameters associated with it. These parameters describe the calling-, trimming-, assembling-, cropping-, and analysis-algorithms of the target. Each Target Parameters specification is created for or corresponding target. The acronym defined in the Target Parameters must be the targets short name.
- Task Entry
- A Sample may contain one or more Task Entries. The number, order and specification of the Task Entries are defined by the Task Template of the Sample's Project. Each Task Entry is defined for one and only one Task Template and there may be only one Task Entry per Task Template.
- Task Template
- Parameter Templates and Parameter Template Groups are hold in Task Templates. Each Task Template may contain a Single Parameter Template or a Group. In addition the Task Template may contain one or more Typings and Conclusions that can be applied to the Typing Results Task Templates are used when defining Projects.
- Trimming
- A read related “hard” cut of reads (as defined in the parameter template or done manually). The results of this operation will be retained during reassembling. Only when doing a reprocessing of reads, trimming will be redone.