SEARCH TOOLS HOME PAGE

APPROX

This program searches for the approximate matches of a given sequences using the Myers fast-bit algorithm.

FREQ
This program has two options: the first one searches for a pattern into a given sequence and displays a graphycal view with all the ocurrences. The second option searches for all the tuples of a given length and displays for each one the graphycal representation .

This tool has been designed by Susana Lopez.
MREPATT and CONREP

Tools to search for consecutive repeated patterns, research project developed with Dr. Juan A. Subirana of the Dep. d'Enginyeria Química.
MREPATT: Consecutive Multiple REpeated PATTerns search tool: given a pattern p, searchs for the exact direct and inverse ocurrences of the patterns p,pp,ppp,... through a set of DNA sequences with simbols A,C,G and T. Also several graphycal representations and mappings are given.

Bioinformatics 19 (18): 2475-2476. (Abstract and Full text)
Supplementary material: preliminary analysis of repeats.
MREPATT has been designed by Roman Roset of Dep. of Software.

CONREPP: CONsecutive REPeated Patterns search tool: given a pattern p, searchs for the exact direct ocurrences of the patterns p,pp,ppp,... through a set of DNA sequences with IUPAC simbols. Also the graphycal representation is given.

CONREPP has been designed by Angel Carreño.
TRANSPO 1.0

From a computational point of view this program searches for the approximate matches of a given sequences whose inverse appears within a given range.

Fromn a biological point of view this program searches for transposons of Class II which are characterized by the existence of terminal inverted repeats, denoted TIR's, that flank the transposons. Then, given the TIR, the program finds all locations at which the direct and inverse TIR approximate matches the DNA sequence and whose distance lies within a given range.

This tool has been designed by Cristina Herraiz.

Reference: N. Santiago, C. Herraiz, J.R. Goñi, X. Messeguer and J.M. Casacuberta. Genome-wide analysis of the Emigrant family of MITEs: of Arabidopsis thaliana
Journal of Molecular Biology and Evolution. 19(12):2285-2293