The method needs no prior, time-consuming alignment of the proteins and therefore an on-the-fly searching of PDB scale crystal structure database for potential bioisosteric replacements is feasible.
In contrast, PAGAN/free and PaPaRa needed 3.3 and 4.7 min for the most time-consuming alignment.
The most popular method for sequence comparison has been to find local alignment pairings using BLAST [ 4] but due to speed limitations, other software has emerged to bypass the time-consuming alignment step by simply counting the number of short sub-sequences shared between a subject and query.
Finally, the energy calculation was deactivated for these tests, as the focus was on the most time consuming part, the alignment.
The signature method can deliver a quick overview of phylogenetic relationships between species in data sets that can be challenging or time consuming for traditional alignment and phylogenetic analysis.
Another possibility to further increase the speed of POTION is to use fast methods to detect groups that are likely to be time consuming (such as alignment length for phylogenetic tree reconstruction) in order to allocate more processors to these groups in the case of parallelized third-party software available for a given step.
We use here the same SVM-regression procedure as RNAz [ 15] to estimate the z-scores from the sequence composition to avoid the time consuming sampling of shuffled alignments.
When the problem instance is large, progressive alignment will be time consuming.
Furthermore, the synchronized nature of WAMS data means that it is ready for immediate use as part of offline applications (e.g. post mortem analysis of events and model validation) without the need for engineers to perform time consuming and error prone manual time alignment.
Without a comprehensive post-alignment tool, analysis can be unnecessarily time consuming and can require specialized programming skills.
This method is, however, far too time consuming because it requires a lot of manual checking during the alignment step.
