Table 1.
The key output files and a brief description of the contents of each. Further descriptions are available through the online help ‘Main Transterm Datafiles’
| ClassSSN-TaxID.complete | Entries with complete CDS (have both inits + terms) |
|---|---|
| A: Lists of entries and identifiers in the redundant and non-redundant sets | |
| *.dat | Data: LOCUS, AccNo, Init [-20,+20], Term [−10,+10], Len, GC3, Nc |
| *.entry | Genbank names without descriptions |
| *.names | List of GenBank names (original input file) |
| *.text | Feature table outputs of TEXT information |
| *.TTSelected | Entries selected by reject_dups criteria |
| B: 5′-UTRs | |
| *.5UTR | 5′-UTRs/flanks, transterm format |
| *.5UTRnrtt | 5′-UTRs/flanks, non-redundant |
| *.5UTRnrtt.fa | 5′-UTRs/flanks, FASTA sequences, non-redundant |
| *.5UTR.fa | 5′-UTRs/flanks, FASTA sequences |
| C: Initiation codon context | |
| *.InitEntries | Entries in.init |
| *.init.fa | Initiation region, FASTA sequences |
| *.init | Initiation region |
| *.initmatrix | GCG consensus output for initiation region (NR) |
| *.initnrttbit | Bit scores for NR initiation region |
| *.initnrttchi | Chi scores for NR initiation region |
| *.initnrttcvs | CVS scores for NR initiation region |
| *.initnrtt.fa | Initiation region, FASTA sequences, non-redundant |
| *.initnrttver | Schneider info. scores, init. region, non-redundant |
| *.initver | Schneider information scores, init. region |
| D: CDS (coding sequences) | |
| *.CDS.fa | Full CDS entries, FASTA sequences |
| *.CDS | Full CDS entries |
| *.CDSnrtt.fa | Full CDS entries, FASTA sequences, non-redundant |
| *.CDSnrtt | Full CDS entries, non-redundant |
| E: Codon usage and bias | |
| *.cod | GCG format of codon usage |
| *.rscu | Output rscu table |
| *.sum | Summary of all the key values |
| F: Termination codon context | |
| *.TermEntries | Entries in.term |
| *.term.fa | Termination region, FASTA sequences |
| *.term | Termination region |
| *.termmatrix | GCG consensus output for termination region (NR) |
| * _termnr.summary | Count_signal of tetramer freq (readable output) |
| * _termnr.tet_tab | Termination tetramer (codon + 3′ base) frequencies |
| * _termnr.tri_tab | Termination trimer (codon) frequencies |
| *.termnrttbit | Bit scores for NR termination region |
| *.termnrttchi | Chi scores for NR termination region |
| *.termnrttcvs | CVS scores for NR termination region |
| *.termnrtt.fa | Termination region, FASTA sequences, non-redundant |
| *.termnrtt | NR version of.term, by old reject_dups criteria |
| *.termnrttver | Info. scores, term. region, non-redundant |
| *.termver | Information scores, term. region |
| G: 3′-UTRs | |
| *.3UTR.fa | 3′-UTRs/flanks, FASTA sequences |
| *.3UTR | 3′-UTRs/flanks |
| *.3UTRnrtt.fa | 3′-UTRs/flanks, FASTA sequences, non-redundant |
| *.3UTRnrtt | 3′-UTRs/flanks, non-redundant |