EGassembler is a web server, which provides an automated as well as a user-customized analysis tool for cleaning, repeat masking, vector trimming, organelle masking, clustering and assembling the of ESTs and genomic fragments.

>EGassembler

Cell Illustrator Online (CIO) enables biologists to draw, model, elucidate and simulate complex biological processes and systems. In conjunction with its outstanding drawing capabilities, CIO allows researchers to model metabolic pathways, signal transduction cascades, gene regulatory pathways and dynamic interactions of various biological entities such as genomic DNA, mRNA and proteins. You can evaluate the Cell Illustrator Online for one month with registration. Cell Illustrator Online Player (viewer of CSML format) is available without registration.

>Cell Illustrator Online

The SSS (Sequence Similarity Search) service integrates BLAST, FASTA,SSEARCH, EXONERATE and TRANS programs into the unified interface to search similar sequences. Major databases supported at Human Genome Center including GenBank, RefSeq, EMBL and UniProt and their subdivisions can be searched.

>SSS

SeqWeb(R) is a web-based sequence analysis package. It is a commercial product of Genetics Computer Group (GCG). This service is open to registered users in the University of Tokyo under the license of GCG. People of U. Tokyo who wants to use this service should contact: register@hgc.jp. SeqWeb provides web access to the most popular Winsonsin Package programs, covering these major areas of sequence analysis.

>SeqWeb

A set of programs for the prediction of subcellular localization of proteis from its amino acid sequence and its origin (e.g., Gram-positive bacteria). Prof. Nakai (HGC) has been involved in all of their development.

>PSORT, PSORT II, iPSORT

Melina is a user-friendly tool to help users to extract a set of common motifs shared by functionally-related DNA sequences. Namely, Melina enables users to compare the motif extraction results of a well-known program with a series of different parameter sets or to compare the results of different algorithms.

>Melina & Melina2

Software for searching transcription factor binding sites (including TATA boxes, GC boxes, CCAAT boxes, transcription start sites (TSS)) using the cut-offs originally estimated by Dr T. Tsunoda (SRC,RIKEN). His algorithm detected local over-representation of transcription factor binding sites and decided the optimum cut-off values for binding scores. Using the optimum cut-off values and transcription factor database TRANSFAC R.3.4 developed by Dr. Wingender et al, the prediction software finds transcription factor binding sites on genomic DNA with low false-negatives and low false-positives particularly for major binding sites besides others.

>TFBIND

Parallel PRRN is a sensitve multiple sequence alignment program originally developed by O. Goto (CBRC, AIST) as prrp/prrn. This version was implemented by Y. Totoki (GSC, RIKEN) to run on a SGI machine in parallel. Its algorithm is the best-first search iterative refinement strategy with tree-dependent partitioning. According to an objective test by a third party, it is one of the most sensitive multiple alignment programs in the world (Thompson et al., 1999).

>Parallel PRRN

PACADE is a deductive database system which searches for protein substructures similar to a given substructure represented as a series of secondary structures. Linked with other systems, PACADE can visualize query and answer substructures. In addition, it can discover features common and specific to the proteins with similar substructures.

>PACADE

Whoin, which is constructed for Genome-hiroba in 2003, is the one of tools to introduce genome science. It just finds query words in human protein sequences.

>whoin

Integrated database system of mapping and sequence data.

>HyperGenome

Software tool to aid contig map construction.

>ContigMaker

Sequence assembler and editor for the nested deletion sequencing method.

>SAND

Genome integrated database retrieval environment.

>Gidre

Structure alignment program for 3D protein structures.

>Stralign

Software for image analysis system for 2D gel electrophoresis of genomic DNA.

>DDGEL

A protein name annotation tool based on PROPER (PROtein Proper-noun Extraction Rules).

>KEX