Biology Reference
In-Depth Information
14. PROMALS3D method generally works best when sequences
are of similar lengths and do not contain large nonhomologous
regions (e.g., inserted nonhomologous domains).
15. Difficult cases that PROMALS3D may not perform well on
include sequences with repeats, duplications or circular permu-
tations, sequences with many disordered regions or low com-
plexity regions, and sequences with predicted transmembrane
segments.
16. Input datasets with many long sequences (e.g.,
1,000 amino
acid residues) may cause memory crash. In these cases,
reduction of the number of pre-aligned groups is recom-
mended, which can be done by setting lower distance cutoff
(-id_thr option) or setting lower maximum number of pre-
aligned groups allowed (-max_group_number option).
>
Acknowledgments
The work is supported in part by the National Institutes of Health
(GM094575 to NVG) and the Welch Foundation (I-1505 to
NVG).
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