Japanese SNPs DB by IMS and JST (Prof. Nakamura's group)

>JSNP

Database of human transcriptional start sites and full-length cDNAs (Profs Sugano and Nakai)

>DBTSS

The open source clustering software contains clustering library that can be used to analyze gene expression data, e.g. microarray data, written with C language. The library consists of hierarchical clustering, k-means, k-medians clustering and 2D self-organizing maps. The software also has wrappers for other languages, e.g. Python and Perl.

>Open source clustering software

BioRuby is a bioinformatics library for the object oriented scripting language Ruby. The library contains useful methods for treating biological databases, sequence analysis softwares and web services to make daily tasks easier and to build automated pipelines of the analysis.

>BioRuby

Cell Illustrator is commercial pathway drawing software that can model and simulate metabolic pathway, gene regulatory network and signal-transduction network for in Silico analyses. The software works under Mac OS X, Windows, Linux and Solaris with Java 5.0 or later environment.

>Cell Illustrator

SiGN-SSM is open source software for estimating dynamic gene networks from short time, replicated, and irregular time interval expression data.It is suitable for analyzing temporal regulatory dependencies between genes. You can download executable binaries for Linux, Mac OS X, and Windows, as well as the source code package that can be compiled for various environments.

>SiGN-SSM

Resources provided at NCBI (National Center for Biotechnology Information) including Genomes, SNP, Taxonomy, GEO etc. in addition to the GenBank, RefSeq, and UniGene databases.

>NCBI

Nucleotide sequence database by EMBL/EBI.

>EMBL

Integrated peptide sequence database by SIB/EBI.

>UniProt

3D structure database by wwPDB (RCSB, EBI, PDBj).

>PDB

Eukaryotic genome database by Sanger/EBI.

>Ensembl

Human genome database by UCSC.

>Golden Path

Pfam : Protein family database by Washington University.
Rfam : RNA family database by Washington University.

>Pfam, Rfam

Integrated protein family database by EBI.

>InterPro

Protein motif and profile database by SIB.

>PROSITE

Eukaryotic promoter database by SIB.

>EPD

Similarity search program package BLAST and its compiled databases.

>NCBI

Similarity search program package FASTA, also including SSEARCH.

>FASTA

ClustalW : Multiple sequence alignment program.
ClustalX : Graphical user interface for the ClustalW.

>ClustalW, ClustalX

Phylogenetic analysis program package.

>PHYLIP

HMMER : Protein family search program by profile hidden Markov models.
INFERNAL : RNA family search program by covariance models.

>HMMER, INFERNAL

Integrated program package for sequence analysis.

>EMBOSS

Protein family search program for the InterPro database.

>InterProScan

exonerate : Generic sequence comparison program including protein to genomic DNA mapping.
Wise2 : Program for comparing a protein sequence to a genomic DNA.

>exonerate, Wise2

Program for discovering motifs within the sequences.

>MEME