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Following software developed in Human Genome Center are available. HGC
ftp server provides mirrors of some databases.

Original Contents

JSNP

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

DBTSS

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

 
 

Mirrored Contents

1000 Genomes

1000 Genomes database (JPT only) by 1000 Genomes Project.

NCBI

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

EMBL

Nucleotide sequence database by EMBL/EBI.

UniProt

Integrated peptide sequence database by SIB/EBI.

PDB

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

Ensembl

Eukaryotic genome database by Sanger/EBI.

Golden Path

Human genome database by UCSC.

Pfam, Rfam

Pfam: Protein family database by Washington University.

Rfam: RNA family database by Washington University.

InterPro

Integrated protein family database by EBI.

PROSITE

Protein motif and profile database by SIB.

EPD

Eukaryotic promoter database by SIB.

 
 
 
 
 
 
 
 
 
 
 

Software provided by other research institutions

NCBI

Similarity search program package BLAST and its compiled databases.

FASTA

Similarity search program package FASTA, also including SSEARCH.

ClustalW, ClustalX

ClustalW: Multiple sequence alignment program.

ClustalX: Graphical user interface for the ClustalW. 

PHYLIP

Phylogenetic analysis program package.

HMMER, INFERNAL

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

INFERNAL: RNA family search program by covariance models.

EMBOSS

Integrated program package for sequence analysis.

InterProScan

Protein family search program for the InterPro database.

exonerate, Wise2

exonerate: Generic sequence comparison program including protein to genomic DNA mapping.

Wise2: Program for comparing a protein sequence to a genomic DNA.

MEME

Program for discovering motifs within the sequences.

 
 
 
 
 
 
 
 
 
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