2007
DOI: 10.1007/s10528-007-9126-6
|View full text |Cite
|
Sign up to set email alerts
|

Evaluation of FORS-D Analysis: A Comparison with the Statistically Significant Stem-loop Potential

Abstract: The stem-loop potential of a nucleic acid segment (expressed as a FONS value), decomposes into base composition-dependent and base order-dependent components. The latter, expressed as a FORS-D value, is derived by subtracting the value of the base composition-dependent component (FORS-M) from the FONS value. FORS-D analysis is the use of FORS-D values to estimate the potential of local base order to contribute to a stem-loop structure, and it has been used to investigate the relationship between stem-loop stru… Show more

Help me understand this report

Search citation statements

Order By: Relevance

Paper Sections

Select...
2
2
1

Citation Types

0
9
0

Year Published

2008
2008
2021
2021

Publication Types

Select...
5
1

Relationship

0
6

Authors

Journals

citations
Cited by 6 publications
(9 citation statements)
references
References 23 publications
0
9
0
Order By: Relevance
“…FORS-M values are calculated by randomizing the natural sequence and taking the average of fold energies, all of which is coded into the software. The code generates 1000 randomized sequences, for the sake of accuracy, although 10 randomizations are known to serve the purpose 12. The FORS-D values are then evaluated by the software by means of the following equation: FONS=FORS-MFORS-D…”
Section: Methodsmentioning
confidence: 99%
See 2 more Smart Citations
“…FORS-M values are calculated by randomizing the natural sequence and taking the average of fold energies, all of which is coded into the software. The code generates 1000 randomized sequences, for the sake of accuracy, although 10 randomizations are known to serve the purpose 12. The FORS-D values are then evaluated by the software by means of the following equation: FONS=FORS-MFORS-D…”
Section: Methodsmentioning
confidence: 99%
“…The code generates 1000 randomized sequences, for the sake of accuracy, although 10 randomizations are known to serve the purpose. 12 The FORS-D values are then evaluated by the software by means of the following equation:…”
Section: Methodsmentioning
confidence: 99%
See 1 more Smart Citation
“…The Monte Carlo procedure can also be simplified to decrease FORS-M computational time [28] using support vector machine-based technology [29]. Our original software ("Bodslp"), written by Professor Jian-sheng Wu [30], retains the Monte Carlo approach and was further developed by Professor Shungao Xu as "Random Fold-Scan" for Windows-based systems [31].…”
Section: Validation Of Four Base Shufflingmentioning
confidence: 99%
“…One method for predicting thermodynamic RNA secondary structure over a viral genome is FORS-D analysis (Forsdyke, 1995;Zhang et al, 2008). A nucleotide segment with a more negative FORS-D value has high potential to develop a stem-loop structure.…”
Section: Introductionmentioning
confidence: 99%