| GenBank
NIH genetic sequence database |
The
EMBL Nucleotide Sequence
Database
|
| GeneCards summary &
links
for each gene |
Database
of
Single Nucleotide Polymorphisms |
| Unigene
: An organized view of the transcriptome |
DDBJ:
DNA Data Bank of Japan |
| Cystic
Fibrosis Mutation Database
|
RefSeq
genomic DNA and transcripts database
|
ENTREZ
Gene Genes and mapped phenotypes
|
Saccharomyces
Genome Database (SGD) |
Fourmidable
database for ant genomics
|
Candida
Genome
Database (CGD)
|
WORMBASE:
the genome of C. elegans
|
ZEBRAFISH
mutation resource
|
GOBASE:
The Organelle Genome Database
|
MGC:
Mammalian Gene Collection
|
|
|
| Gene
sequence search and alignment servers |
|
|
|
BLAST
- Pasteur
Institute
|
BLAST at NCBI
|
| BLAST
- EMBL |
BiSearch
BiSearch is a primer-design algorithm for
DNA sequences |
| BLAST
- NIAS
DNA Bank |
BLAST
- ExPasy
(Switzerland) |
| FASTA
- GeneStream
IGH Montpellier |
FASTA
- DDBJ
(Japan) |
| FASTA
- DISC/AFFRC |
EMBOSS
Matcher: Waterman-Eggert algorithm
alignment |
| KEGG
GENES Genes in high-quality genomes |
PARALIGN:
sequence similarity search |
| FramePlot
- Protein Coding Region Prediction in
Bacterial DNA |
ORF
Finder - Open Reading Frame Finder
at - NCBI
(US) |
| Translate
- Translates a nucleotide sequence to a
protein sequence |
Transeq
- Nucleotide to protein translation |
| Align Pairwise
global and local alignment tool WSEmboss |
CpG
Plot/CpGreport CpG
Island finder and plotting tool WSEmboss |
| Pepstats/Pepwindow/Pepinfo EMBOSS
programs for basic protein sequence
analysis WSEmboss |
OMA browser:
orthology prediction server |
| Genewise DNA
search
accomodating introns and frame-shifting |
NeedleN
sequence alignment |
| smiRNAdb
- Mammalian small RNAs |
(Reverse)-Transcription
and
Translation Tool |
| IMGT
- ImMunoGeneTics db |
EPD
- Eukaryotic Promoter db |
| KEGG
GENOME Genomes in organisms |
Secondary
Structure
Alignment tool
|
EMBOSS
Supermatcher for local pair-wise
alignments
|
|
|
|
|
|
|
|
| Protein
sequence servers |
|
|
|
UniProtKB
Protein sequence
database
|
Chordata
protein annotation program |
| KEGG
GENES Genes and proteins |
MSA Multiple
Sequence Alignment |
SwissAlign
Protein sequence alignment with
Smith-Waterman algorithm
|
ScanSite:
Search biological databases for regular
expressions
|
| Radar
- Repeat detection in protein sequences |
REPRO
- Repeat detection in protein sequences |
| HMMER:
sequence analysis with hidden Markov
models |
DAS
predicts transmembrane segments by "Dense
Alignment Surface" method |
| Anchor identifies
protein segments
that
reside in disordered regions |
TRUST
- Repeat detection in protein sequences |
| HeliQuest
- helix prediction server |
XSTREAM
- Repeat detection and architecture
modeling in protein sequences |
| PATTINPROT
Pattern search server |
Hits
- Protein sequence to motifs server |
| ProFound
- Search known protein sequences with
peptide mass information |
PRINTS:
Protein fingerprint server |
| ProteinProspector
- Tools for peptide mass data |
Mascot
- Peptide mass fingerprinting |
| SMART
- Simple Modular Architecture Research
Tool |
ELM
- resource for finding functional
sites in proteins |
| HAMAP:
High-quality Automated and Manual
Annotation of microbial Proteomes |
PPSEARCH
- Scans a sequence against PROSITE |
| InterPro
- Integrated Resources of Proteins Domains
and Functional Sites |
ViralZone
- Portal to viral UniProtKB/Swiss-Prot
entries |
| PRINTS
- Protein Motif fingerprint db |
Gene3D
- Structural and Functional Annotation of
Protein Families |
| CYSREDOX
Cysredox predicts the redox state of
cysteins in proteins |
PIRSF
- Protein classification system |
| PSORT-B
for
prediction of localization in
Gram-negative bacterial proteins |
DAS-TMfilter
predicts transmembrane segments by "Dense
Alignment Surface" method |
PFAM
protein family annotations
|
BOXSHADE:
Pretty printing of multiple alignment
files
|
|
|
|
|
|
|
| Protein
3D structure servers |
|
|
|
RCSB
Protein Data
Bank
|
Worldwide
Protein Data Bank |
| PDBsum
is an at-a-glance overview of PDB
structures |
DECOMP
is a PDB protein-ligand decomposition
server |
| WikiPDB
is a social site for improving and
annotating PDB, external API's allowed |
PDBWiki
is a PDB annotation tool |
| iPfam:
protein domain interactions database |
PDBj
Protein Data Bank Japan |
CCDC
Cambridge Crystallographic Data Center
|
HCA
Hydrophobic cluster database |
GENO3D:
Automatic modeling of 3d protein
structures
|
FoldAlign:
RNA fold predictor |
| SWISS-MODEL
- An automated protein modelling server |
TopPred
- Topology prediction of membrane proteins |
| HMMTOP
- Prediction of transmembrane helices and
topology of proteins |
TMpred
- Prediction of transmembrane regions and
protein orientation |
| PDBTM
is a transmembrane protein selection tool
from the PDB. |
TOPDOM
a collection of domains and sequence
motifs located conservatively in one side
of transmembrane proteins |
| SOSUI
- Prediction of transmembrane regions |
TMHMM
- Prediction of transmembrane helices in
proteins |
| Paircoil
- Prediction of coiled regions in proteins
|
Paircoil2
- Prediction of the parallel coiled
regions of proteins |
| Multicoil
- Prediction of multi-stranded coiles |
STRAP
- A structural alignment program for
proteins |
| AGADIR
- to predict the helical content of
peptides |
TopMatch-web
- Structure comparison of proteins |
| TLSMD
- Protein flexibility prediction |
GlobPlot
- Protein
disorder/order/globularity/domain
predictor |
| DisEMBL
- Protein disorder prediction |
MeDor
- Metaserver or Disorder |
| POODLE
- Prediction Of Order and Disorder by
machine LEarning |
DAS
- Prediction of transmembrane regions |
| TatP
- Twin-arginine signal peptides |
TargetP
- Prediction of subcellular location |
| IUPred
Prediction of Intrinsically Unstructured
Proteins |
SCIDE
identifies the stabilization center
residues in known protein structures |
| SCPRED predicts
stabilization
center
residues in proteins with unknown
structure |
SRide identifies
the
stabilizing residues in proteins |
| TMDET:
the detection of the transmembrane regions
of membrane proteins by using their 3D
structure only |
TOPDB
a collection of transmembrane protein
datasets containing experimentally derived
topology informat |
|
|
|
|
|
|
| Protein interaction network servers |
|
|
|
| DIP
- Database of Interacting Proteins |
NASCENT
PPI network generation
tool
|
| HPRD
- Human Protein Reference Database |
IntAct
Interacting proteins database |
| BioGRID
- General Repository for Interaction
Dataset |
PPI
- Jena Protein-Protein Interaction db |
| BOND
- Biomolecular Object Network
Databank |
MINT
- Molecular INTeraction
database
|
| NetworkBLAST
finds complexes in PPI networks that are
conserved in evolution |
IsoRank:
Global PPI network alignemnt tool |
| TrypanoPPI:
Trypanosome target prediction based on PPI
network analisys |
MIPS
Mammalian Protein-Protein Interaction
Database |
| Homomint
is a human entry point to MINT |
APID
Agile Protein Interaction Data Analyzer |
| DP-Bind sequence-based
prediction of DNA-binding residues in
DNA-binding proteins. |
SNAPPI structures
and
interfaces for protein interactions |
| ICBS A
database
of PPIs mediated by interchain �-sheet
formation |
| HIV
PI
Database Interactions between
HIV and host proteins at the NCBI |
MIPS
CYGD
Saccharomyces cerevisiae genome
database |
iPfam:
protein domain interactions database
|
|
|
|
| Metabolic networks and metabolomics
servers |
|
|
|
UniPathway
- Metabolic pathways
database
|
KEGG
PATHWAY Pathway maps for systemic
functions
|
| KEGG
RCLASS Reaction class |
KEGG
RPAIR Reactant pair chemical
transformations |
| KEGG
ENZYME Enzyme nomenclature |
KEGG
PATHWAY Pathway maps |
| KEGG
COMPOUND Metabolites and other small
molecules |
Human
Meatabolome Database (HMDB)
|
Golm
metabolome database
|
Metabolome
Express: a forum for metabolomics
data
|
Serum
Metabolome
Database of the human serum
|
Tumor
metabolome server
|
ExPASy
biochemical pathways is the
digitized version of the Roche wallchart
|
ChemMine
metabolomic compound mining db
|
MetaCyC metabolic
pathways
|
ChEBI
compound database
|
Plant
Metabolic Network (PMN) pathways
|
|
|
|
| Nanobiotechnology
servers |
|
|
|
BROWNIAN:
3D Brownian motion simulator
|
|
|
|
Metagenomics and phylogeny
servers
|
|
|
|
Biology
WorkBench: an integrated tool
for sequence alignment and phylogeny
|
MG-RAST:
metagenomics analysis server
|
Web
MGA: webserver for
metagenomics analysis
|
AmphoraNet:
Phylogenetic annotation of metagenomic
sequences
|
Real
Time Metagenomics annotation
|
|
|
|
| Other directories of LifeSci servers |
|
|
|
| List
of
Protein Disorder Predictors |
KEGG:
Kyoto Encyclopedia of Genes and Genomes |
ExPASy
Tools
|
ENTREZ
cross-database search |
| BioSpider:
a bio search engine |
|
The
Peptide
Resource Page
|
|
|
|
