Free Energy - A program intended for computation of Gibbs free energy distribution in DNA sequence.
Name and version:
FreeEnergy, version 2.3.0
Author and institution:
Matej Stano
Institute of Molecular Biology, Slovak Academy of Sciences
Description and Usage:
Program FreeEnergy was created for computation and graphical interpretation of Gibbs free energy distribution in DNA sequence. Free energy of a DNA fragment is calculated as a sum of partial free energies of closest-neighbour dinucleotides. FreeEnergy may be used for prediction of prokaryotic promoter localization.
It accepts query DNA sequence in FASTA, GenBank and Raw format and is case-insensitive. Only single sequence can be inserted for analyse.
User has to define one parameter: Size of sliding-window. This parameter refers to range of the sequence segment, the free energy is computed within during each computational step. Proper setting of this parameter is critical to obtain relevant results. The default value for Size of sliding-window is 50 nts, but it should be reseted according to character and length of analyzed sequence as well.
Program provides graphical and numerical results. Graphical results are represented by a line graph of free energy distribution in DNA sequence. Regions with lower ΔG values are thermodynamically less stable. Prokaryotic promoters are usually localized in these regions.
Numerical results are individual ΔG values (used for graph plotting), length of analyzed sequence, average ΔG value and GC content in sequence.
Requirements:
Analyzed sequence has to be in FASTA, GenBank or Raw sequence format.
FASTA format:
>gnl|em|HSFAU (X65923) H.sapiens fau mRNA
ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc
agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg
cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc
tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc
tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc
gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga
agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca
cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc
tctaataaaaaagccacttagttcagtcaaaaaaaaaa
GenBank format:
LOCUS HSFAU
ACCESSION X65923
DEFINITION H.sapiens fau mRNA
BASE COUNT 125 a 139 c 148 g 106 t
ORIGIN
1 ttcctctttc tcgactccat cttcgcggta gctgggaccg ccgttcagtc gccaatatgc
61 agctctttgt ccgcgcccag gagctacaca ccttcgaggt gaccggccag gaaacggtcg
121 cccagatcaa ggctcatgta gcctcactgg agggcattgc cccggaagat caagtcgtgc
181 tcctggcagg cgcgcccctg gaggatgagg ccactctggg ccagtgcggg gtggaggccc
241 tgactaccct ggaagtagca ggccgcatgc ttggaggtaa agttcatggt tccctggccc
301 gtgctggaaa agtgagaggt cagactccta aggtggccaa acaggagaag aagaagaaga
361 agacaggtcg ggctaagcgg cggatgcagt acaaccggcg ctttgtcaac gttgtgccca
421 cctttggcaa gaagaagggc cccaatgcca actcttaagt cttttgtaat tctggctttc
481 tctaataaaa aagccactta gttcagtcaa aaaaaaaa
Raw format:
ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtc
gccaatatgcagctctttgtccgcgcccaggagctacacaccttcgaggt
gaccggccaggaaacggtcgcccagatcaaggctcatgtagcctcactgg
agggcattgccccggaagatcaagtcgtgctcctggcaggcgcgcccctg
gaggatgaggccactctgggccagtgcggggtggaggccctgactaccct
ggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc
gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaag
aagaagaagaagacaggtcgggctaagcggcggatgcagtacaaccggcg
ctttgtcaacgttgtgcccacctttggcaagaagaagggccccaatgcca
actcttaagtcttttgtaattctggctttctctaataaaaaagccactta
gttcagtcaaaaaaaaaa
Value of the parameter Size of sliding-window has to be defined!
Value of the parameter Size of sliding-window has to be lesser than length od analyzed sequence!
Value of the parameter Size of sliding-window has to be at least 2!
Diagnostics:
If message „Inserted sequence contains inacceptable characters!“ appears, inserted sequence contains other letters than A, C, G ot T.
If message „Define parameter properly!“ appears, then parameter Size of sliding-window was not defined correctly (do not respect criteria mentioned in Requirements).