Analysis

Sequence Similarity Searches

Basic Local Alignment Search Tool(BLAST) at NCBI

Blast Database Searches at EBI

NCBI BLAST Search with Entrez and SRS Links

ISREC WU-BLAST server

Advanced BLAST2 Search with post-processing at EMBL

FASTA homology searches

BLITZ ultra-fast protein databases searches

Sequence Interpretation Tools(GenomeNet WWW server- Japan)

www2.ebi.ac.uk

---

PROSITE pattern searches

EBI

EXPASY

IBCP

---

Alignment

ClustalW Multiple Sequence Alignment

---

Primary structure analysis

HLA_Bind - Prediction of MHC type I (HLA) peptide binding

SYFPEITHI - A DATABASE OF MHC LIGANDS AND PEPTIDE MOTIFS (Ver. 1.0)

ProtParam - Physico-chemical parameters of a protein sequence (amino-acid and atomic compositions, pI, extinction coefficient, etc.)

Antigenic : Find antigenic sites in proteins (EMBOSS)

---

Hydrophilicity/Hydrophobicity Search and Comparison 

Protein Hydrophilicity/Hydrophobicity Search and Comparison Server

---

Antibody Resources

Antibody Resource Page

AbCheck - Antibody Sequence tester

---

Others

ExPASy Proteomics tools

Genemark Program

Codon Usage Tabulated from Genbank

Compute pI/Mw tool

BCM Gene Finder

GeneQuiz server homepage

GeneFIND Family Identification System(University of Texas Health Center at Tyler)

Primer

Signal Scan

Promoter Scan

TRANSFAC (-database sequence analysis tools)

The CMS Molecular Biology Resource

Computing applied to Biomolecules and Genomes , France