BIOINFORMATICS SOFTWARE

CORRELATION FINDER

CORRELATION FINDER is a free software which allows to seek correlations between nucleotides in genomic sequences. It computes some parameters for each analyzed correlation: the relative abundance, the conditional probability, the frequency of the words making up the correlation. It is quite fast because utilizes a buffer to keep data red from input file to minimize accesses to hard disk.

Download complete ZIP archive: Correlation_finder.zip

Download files singularly: Correlation_finder.exe, correlation_finder.chm, correlation_finder.hhp, fasta_input.fas, plain_text_input.txt, output.txt,  CorrelationFinderHelp.pdf.

REFERENCES: 

Piva F, Principato G
CORRELATION FINDER.
In Silico Biol. 2005 Sep 24;5(4):0042 [Epub ahead of print]
PMID: 16268790 [PubMed - as supplied by publisher]

RANDNA: A RANDOM SEQUENCE GENERATOR  

RANDNA is a free software which allows to create random DNA sequences setting both their length and the percentage of nucleotide composition. Random number generator of Delphi 6 is used, it guarantees an uniform distribution of random numbers, a good randomness, a long cycle length and a high spped. This tool is useful for Monte Carlo calculations and also to calculate the background score of an alignment. Its graphic interface allows to easily set the parameters and it can generate sequences up to 4 thousand millions in length. It runs on the Windows operative system.

Download complete ZIP archive: RANDNA.zip

Download files singularly: RANDNA.exe, RANDNA_article.doc, RANDNA_help.chm, RANDNA_help.pdf 

PATTERN DISCOVERY TOOL is a free software which allows to seek exhaustively patterns both short and very spread, in genomic sequences. User can set the kind of pattern to search: number of words making up pattern, their maximum length, minimum and maximum distance among them. It is very fast because utilizes a buffer to keep data red from input file to minimize accesses to hard disk but also it has been rebuilt and optimized some indexing function to the strings. Its graphic interface allows to easily set the parameters that characterize the motifs being sought. This tool handles very large data sets and runs on the Windows operative system. 

Download complete ZIP archive: Pattern_discovery.zip

Download files singularly: Pattern_discovery.exe, Pattern_discovery.chm

WORDS VIEWER

WORDS VIEWER is a free software which allows to see the distribution of motifs in a group of nucleotide sequences. It shows the occurrence of words choosen by user in a normalized sequence length, so it is possible to work with sequences of different length. Its graphic interface allows to easily set the parameters that characterize the motifs being sought. This tool handles large data sets and runs on the Windows operative system. 

Download complete ZIP archive: Words_viewer.zip

Download files singularly: Words_viewer.exe, Words_viewer.chm

Author: Eng Francesco Piva

Institute of Biology and Genetic
Polytechnic University of Marche
Via Brecce Bianche
Monte D'Ago
60131 ANCONA
ITALY