Nucleotide Analysis
NUCLEOTIDE ANALYSIS
TABLE OF CONTENTS
Version 8.1-UNIX
Printed: April 22, 1996 15:51
Melting temperature and GC content of a sequence can be analyzed and displayed on a plot. The variation in di-nucleotide composition along a sequence can be plotted.
Melt
Melt calculates the melting temperature (Tm) and the percent G+C of a nucleic acid sequence using the algorithms described by Breslauer et al. Proc. Natl. Acad. Sci. USA 83, 3746-3750 and Baldino et al. Methods in Enzymol. 168, 761-777.
MeltPlot (+)
MeltPlot plots the melting curve for a nucleic acid sequence using the algorithms described by Breslauer et al. Proc. Natl. Acad. Sci. USA 83, 3746-3750 and Baldino et al. Methods in Enzymol. 168, 761-777.
BasePairPlot (+)
BasePairPlot plots the percentage occurence and the observed over expected frequency of a di-nucleotide pair relative to their position in a nucleic acid sequence.
CpGPlot (+)
CpGPlot plots the frequency of occurence of CpG di-nucleotides and C and G percentage relative to their position in a sequence by the method described by Gardiner-Garden (1987)
CpGReport *
CpGReport looks for potential CpG islands in a nucleotide sequence.
Chaos (+)
Chaos makes a CHAOS game representation of a nucleic acid sequence using the method of Jeffrey (1990) Nucleic Acids Research 18: 2163-2170.
CodFish *
CODFISH calculates a set of codon usage statistics for a sequence using a specified codon usage table.
WordCount *
WordCount counts the commonest words in a sequence and reports them in order of frequency and sequence.
WordUp *
WordUp is based on a first order Markov analysis and detects statistically significant oligonucleotide patterns from six to nine nucleotides long in the sequences under investigation. WordUp dynamically detects significant signals of any length in the same analysis.
Poland (+)
The program Poland simulates transition curves of double-stranded nucleic acids (DNA as well as RNA). Calculation is based on Poland, D. (1974) 'Recursion Relation Generation of Probability Profiles for Specific-Sequence Macromolecules with Long-Range Correlations'.
GeneTrans
GeneTrans extracts and/or translates coding regions as defined in the feature table of sequences stored in the EMBL or Genbank databases.
GapFrame
GapFrame moves all gaps in a DNA sequence reading frame to be at codon boundaries.
Prima * (+)
Prima selects oligonucleotide primers for a template DNA sequence. The primers may be useful for the polymerase chain reaction (PCR) or for DNA sequencing. You can allow Prima to choose primers from the whole template or limit the choices to a particular set of primers listed in a file.
QuickTandem *
QuickTandem scans for potential tandem repeats in a nucleotide sequence.
Tandem *
Tandem looks for multiple tandem repeats of a given size in a nucleotide sequence.
Inverted *
Inverted looks for imperfect inverted repeats in a nucleotide sequence.
EComposition *
EComposition determines the composition of sequence(s). For nucleotide sequence(s), EComposition also determines dinucleotide and trinucleotide content.