Biocomputing WWW services

Databanks screening:

a) by similarity
 
BLAST at NCBI
Fasta3  at EBI, United Kingdom
MPsrch  (Smith-Waterman algorithm) at EBI, United Kingdom
Search against the Pham library of HMM profiles

b) by names, definitions, keywords etc.

Entrez at NCBI
SRS (Sequence Retrievial System) at EBI,  DKFZ , HGMP,  CNB,  Infobiogen,  CAOS-CAMM
EFETCH : quick database entry retrievial (by entry name or accession  number) at Institute Pasteur ( advanced form )

Alignment:

ClustalW Multiple Sequence Alignment  at  EBI
ClustalW   ( advanced form ) at Institute Pasteur
DIALIGN
Match-Box at University of Namur, Belgium
Global multiple alignment (Bio-lirmm, France)
ToPLign : standard pairwise and multiple alignment methods with flexible parameter handling
SIM : pairwise alignment of protein sequences (ExPASy, Switzerland)
 

Other:

READSEQ : sequence format conversion ( advanced form )
Webcutter 2.0 (USA): restriction enzymes simulation
MFold (Washington University School of Medicine, USA): RNA secondary structure prediction
RNA analysis : mfold, RNAfold (Vienna package), tRNAscan-SE, FAStRNA; Institute Pasteur
Primer3 (MIT, USA): design PCR primers
Secondary structure prediction for proteins (Bio-lirmm, France)
Search Genes and Coding Regions (Institute Pasteur)
Phylogeny : PHYLIP, fastDNAml, Molphy (Institute Pasteur)
Protomap :  an automatic hierarchical classification of all SwissProt proteins. (Hebrew University, Israel)
Pattern Search and Discovery : Prosearch, ProDom, TACG, PLSEARCH,   BLIMPS, MEME, PrattWWW, HMMER, PFTOOLS (Institute Pasteur)
ISREC ProfileScan Server
MELTING : for an oligonucleotide: enthalpie, the entropy and melting temperature of the binding to its complementary template (Institute Pasteur)

Service at EMBL (Germany)

Service at EBI (United Kingdom)

Service at Institute Pasteur  (France)

Service at ExPASy  (Switzerland)

Service at Laboratory of Theoretical Genetics  (Novosibirsk, Russia)

GeneBee service

Catalogues of online bioinformatic services:

ONLINE ANALYSIS TOOLS  (Dr. Andrew Kropinski, Kingston, Canada)
 Selected links with comments and instructions.
 
Catalogue of WWW services (based on EMBL site)
 
Multiple Alignment Resource Page