Notes on nucleotide range:

You can compare the alternate model against the null model over the whole input alignment if you like (e.g. a virus genome alignment). However, if the query ORF is only a relatively small region in the genome, then you will probably get better statistics if you limit the nucleotide range investigated to just encompass the query ORF. Outside the query ORF, the null and alternate models are essentially identical (although the likelihood scores may differ slightly due to different fitted t values - more-or-less evolutionary time - for the two models). Therefore the likelihood ratio for each nucleotide in this region will be uninformative. These uninformative values can make interpretation of the final summed-over-sequence statistics confusing, and will 'dilute' the coding signature (if it exists) of the query ORF.

However, if your query ORF is fairly short (e.g. < 40 codons) then you may want to take a larger nucleotide range, encompassing the query ORF. This is because, for short regions, there may not be enough nucleotide mutations to accurately determine t for either the null or alternate models.

Since alignments may be poorer at the ends of a reference sequence ORF (e.g. if the ORF utilizes a later start or earlier stop codon in other sequences), sometimes you may want to set the nucleotide range to a smaller region than the reference sequence ORF. In this case, we suggest that first you enter the whole reference sequence ORF. Then you can use the nucleotide-by-nucleotide plot on the results page to check for stops in the non-reference sequences, and reduce the nucleotide range accordingly in a second run.


Dependence on 'Operating mode':

Test input query CDSs: Here you can use any of the three nucleotide range options. The recommended option is 'Only use nt within query CDS(s)', unless the query CDS is less than about 40 codons (depending on the number of sequences and their total divergence) in which case you may want to use the 'Use a given nucleotide range' option to specify a region of about 40-100 codons length, encompassing the query ORF. The models will be fitted, and statistics calculated only within the query CDS(s) (which may be disjoint).

Note that if the 'Use a given nucleotide range' option is selected, and the first number is greater than the second, then the two numbers will be swapped round. I.e. you can't use this option to cross the 'boundary' on a circular genome. Instead you can use the 'Only use nt within query CDS(s)' option with a 'Query CDS' such as, for example, 'join(2000..3000,1..1000)'.

Find and test all non-annotated ORFs: Whichever of the three options is selected, the region used for calculating statistics for each located ORF is just the ORF itself. Instead the nucleotide range options are used to select the range for ORF detection. If the 'Use whole sequence' option is selected, then the whole sequence will be used for ORF detection. If the 'Use a given nucleotide range' option is selected, then only ORFs within that range will be used. If the 'Only use nt within query CDS(s)' option is selected, then it will default to the 'Use whole sequence' option.

Six-frame sliding window plots: Whichever of the three options is selected, the region used for calculating statistics for each window is just the window itself. Instead the nucleotide range options are used to select the range for which six-frame sliding window plots will be produced. If the 'Use whole sequence' option is selected, then six-frame sliding window plots will be produced for the whole sequence. If the 'Use a given nucleotide range' option is selected, then six-frame sliding window plots will be produced only for the given region. If the 'Only use nt within query CDS(s)' option is selected, then it will default to the 'Use whole sequence' option.