Web Tools for  Analysis of
DNA Sequence and Structure


PATTERNFINDER searches DNA sequences for matches to specific or flexible patterns. Flexible patterns include consensus sequences containing ambiguous nucleotides and unspecified nucleotides (N's), or multiple specific patterns separated by a variable number of N's, or simple sequences that are repeated a variable number of times. A batch mode generates a tabular map of matches to multiple, different patterns. Sequences flanking pattern matches can be analyzed to identify those with a low free energy for DNA unwinding. The program is useful in characterizing REGULATORY REGIONS for TRANSCRIPTION, REPLICATION and other processes and may predict functional DNA UNWINDING ELEMENTs (DUEs). See the readme file for details.

WEB-THERMODYN computes the DNA helical stability across regions of DNA sequences using a sliding-window-analysis. It can be used to identify easily unwound DNA sequences which, when present in a REPLICATION ORIGIN, could function as a DNA UNWINDING ELEMENT (DUE). See the readme file for details.

THERMOCALC2 computes and compares the helical stabilities of two duplex DNAs of equal length. It is useful for calculating the change in helical stability when MUTATIONS are introduced into a wild type DNA sequence, as in the case of linker scanning mutagenesis of REPLICATION ORIGINS to search for DUEs. See the readme file for details.

THERMOCALC1 computes the helical stability of duplex DNA using DNA sequence information. See the readme file for details.

Questions or comments:  David.Kowalski@RoswellPark.org