Bioinformatics Tools

BLAST(Regular BLAST, Mega BLAST, BLAST 2 sequences, BLAST HELP MANUAL) stands for Basic Local Alignment Search Tool and was developed by Altschul et al. (1990) and significantly improved by Altschul et al. (1997). It is a very fast search algorithm that is used separately for protein or DNA databases. and is best used for sequence searching, rather than for motif searching. REDB provides BLAST facility for the rice. To search other datasets and access further information on BLAST resources, help document and BLAST 2.0 Release, please refer to http://www.ncbi.nlm.nih.gov/BLAST/.

VectorScreen is a tool for identifying segments of a nucleic acid sequence that may be of vector, which was developed to combat the problem of vector contamination in sequence databases.

Genome Browser is a Web-based application for displaying genomic annotations and other features. The reference annotation layer consists in the 12 rice pseudomolecules released by the TIGR (Version 5.0, January 24, 2007)

Readseq is particularly useful as it automatically detects many sequence formats, and interconverts among them.

ClustalW is a general purpose multiple alignment program for DNA or proteins.

Primer3 Easy to design primers, developed by the Whitehead Institute for Biomedical Research.

SSRSCAN Search for simple sequence repeats in FASTA-formatted DNA sequences

GENSCAN which offers complete gene prediction, in that it uses a number of different algorithms to predict introns, exons (leading, internal, and terminal), donor and acceptor splice sites, and polyadenylation sites. The highest scoring arrangement of these categories are then used to predict actual gene composition

Map Viewer (Beta1) is a tool developed at REDB to view the markers in different maps.

Local EST Browser

Enter AC NO.:(e.g. EI#01-A02)

AC Convert